CassavaBase

Upload an experimental field trial into the database that you have saved on your computer in Excel

Design a completely new experimental field trial in the database

Catalog your available seed inventory into the database

Upload phenotypic data into the database that you have saved on your computer in Excel

Plan tissue sampling

Upload crosses and crossing information into the database

Print barcode labels for my experiment (for your plots or plants or tissue samples in the field, or for your 96 well plate and tissue samples)

Analyze phenotypic performance across trials

Prepare a 96 or 384 well plate for a genotyping experiment

Upload VCF genotypic data

Intro
Sampling Level
Select a field trial
Plant Entries
Create Tissue Sample Entries

This workflow will guide you through tissue sampling an experiment

Tissue samples collected from the field are linked to a single plant, which is in turn linked to a single plot.

Many tissue samples can be created for each plant.

Each tissue sample has a globally unique name.

A unique tissue sample is present in each well of a genotyping plate (96 or 384 well plates).

The tissue sample in a 96 well plate can originate from another tissue sample name, plant name, plot name, or accession name.
At which level do you plan to keep track of your sampling?
   Accession Level: The sample is not from a field trial entity and only the accession name is known.
   Plot Level: Each plot in the field has a unique identifier, ideally with a barcode label.
   Plant Level: Each plant in the field has a unique identifier, ideally with a barcode label.
   Tissue Sample Level: Each tissue sample collected from the field has a unique identifier, ideally with a barcode label.

Select a field trial

Plant entries in your field trial

Plant entries not relevant for the type of tissue sampling you selected. Go to next step.

Plant entries exist for this trial. Go to next step.

Please create plant entries for this trial.

Number of plants per plot:

Inherits Management Factor(s) From Plots:
Create tissue sample entries for this trial

Field trial tissue sample entries not relevant for the type of tissue sampling you selected. Go to next step.

Tissue sample entries exist for this trial. Go to next step.

Number of tissue samples per plant:

Inherits Management Factor(s) From Plots:

Complete! You have all the entities you need to conduct your sampling.

All of the entities that you want to sample are saved in the database and available to use!
You can print barcodes for the entities you intend to sample on. These barcodes can be attached to your collection vials/containers to assist during sampling.

After you have finished sampling, you can use these entities as source material for a genotyping plate (96 or 384 well plate). Click the button below to create a genotyping plate now, if you will create a 96 or 384 well plate.
The Android Coordinate application can help you create 96 or 384 well plates. Alternatively you can create your plate layout in Excel and upload it.

Complete! You have all the entities you need to conduct your sampling.

All of the entities that you want to sample are saved in the database and available to use!
You can print barcodes for the entities you intend to sample on. These barcodes can be attached to your collection vials/containers to assist during sampling.

After you have finished sampling, you can use these entities as source material for a genotyping plate (96 or 384 well plate). Click the button below to create a genotyping plate now, if you will create a 96 or 384 well plate.
The Android Coordinate application can help you create 96 or 384 well plates. Alternatively you can create your plate layout in Excel and upload it.

Trials may be uploaded in an Excel file (.xls or .xlsx)

Stock type being evaluated in this trial: accession

plot_name	accession_name	plot_number	block_number	is_a_control	rep_number	range_number	row_number	col_number	seedlot_name	num_seed_per_plot	weight_gram_seed_per_plot	entry_number

Stock type being evaluated in this trial: cross unique id

plot_name	cross_unique_id	plot_number	block_number	is_a_control	rep_number	range_number	row_number	col_number	seedlot_name	num_seed_per_plot	weight_gram_seed_per_plot	entry_number

Stock type being evaluated in this trial: family name

plot_name	family_name	plot_number	block_number	is_a_control	rep_number	range_number	row_number	col_number	seedlot_name	num_seed_per_plot	weight_gram_seed_per_plot	entry_number

Required fields:

accession_name or cross_unique_id or family_name (must exist in the database. This is the accession or cross unique id or family name being tested in the plot.)
plot_number (a sequential number for the plot in the field (e.g. 1001, 1002, 2001, 2002). These numbers should be unique for the trial.)
block_number (a design parameter indicating which block the plot is in)

Optional fields:

plot_name (must be unique across entire database. If not provided in the file, it will be automatically generated as {trial_name}-PLOT_{plot_number}.)
is_a_control (type 1 in this field if the plot is a control, otherwise leave blank. generally you will have accessions/cross unique ids/family names that are controls, so you should indicate the plots of those accessions/cross unique ids/family names as a control.)
rep_number (replicate number, numeric)
range_number (range number. often synonymous with col_number, numeric)
row_number (row number. If the field is a grid, this represents the y coordinate, numeric, required for field map generation.)
col_number (column number. If the field is a grid, this represents the x coordinate. Sometimes called range_number, numeric, required for field map generation.)
seedlot_name (the seedlot from where the planted seed originated. Must exist in the database)
num_seed_per_plot (number seeds per plot. Seed is transferred from seedlot mentioned in seedlot_name. Numeric)
weight_gram_seed_per_plot (weight in gram of seeds in plot. seed is transferred from seedlot mentioned in seedlot name. Numeric)
entry_number (a trial-level entry number assigned to the stock. Numeric)

Treatments:

treatment columns (additional column(s) that specify the name of a treatment (e.g. inoculated, drought, etc). The value for each plot should be 1 if the treatment was applied or empty.)

Only the required fields are necessary to include in the upload template. You may add any additional optional fields. The fields can be in any order.

Multiple Trial Designs:
Header:
The first row (header) must contain the following, which is an expansion of the single trial design header:

trial_name	breeding_program	location	year	transplanting_date	design_type	description	trial_type	trial_stock_type	plot_width	plot_length	field_size	planting_date	harvest_date	plot_name	accession_name	plot_number	block_number	is_a_control	rep_number	range_number	row_number	col_number	seedlot_name	num_seed_per_plot	weight_gram_seed_per_plot	entry_number

Header as a string:

trial_name,breeding_program,location,year,transplanting_date,design_type,description,trial_type,trial_stock_type,plot_width,plot_length,field_size,planting_date,harvest_date,plot_name,accession_name,plot_number,block_number,is_a_control,rep_number,range_number,row_number,col_number,seedlot_name,num_seed_per_plot,weight_gram_seed_per_plot,entry_number

Required fields:

trial_name (Must be unique across entire database. It is often a concatenation of the year, transplanting_date, purpose, unique number, and location.)
breeding_program (The name of breeding program that managed the trial, must exist in the database.)
location (The name or abbreviation of the location where the trial was held, must exist in the database.)
year (The year the trial was held.)
design_type (The shorthand for the design type, must exist in the database. Possible values include CRD (Completely Randomized Design), RCBD (Randomized Complete Block Design), RRC (Resolvable Row-Column), DRRC (Doubly-Resolvable Row-Column), URDD (Un-Replicated Diagonal Design), ARC (Augmented Row-Column), Alpha (Alpha Lattice Design), Lattice (Lattice Design), Augmented (Augmented Design), MAD (Modified Augmented Design), greenhouse (undesigned Nursery/Greenhouse), splitplot (Split Plot), stripplot (Strip Plot / Split Block), p-rep (Partially Replicated), Westcott (Westcott Design))
description (Additional text with any other relevant information about the trial.)
accession_name OR cross_unique_id OR family_name (The accession, cross, or family being tested in the plot, must exist in the database.)
plot_number (A sequential number for the plot in the field (e.g. 1001, 1002, 2001, 2002). These numbers should be unique for the trial.)
block_number (A design parameter indicating which block the plot is in.)

Additional optional fields:

plot_name (Must be unique across entire database. If not provided in the file, it will be automatically generated as {trial_name}-PLOT_{plot_number})
trial_type (The name of the trial type, must exist in the database. Possible values include Seedling Nursery, phenotyping_trial, Advanced Yield Trial, Preliminary Yield Trial, Uniform Yield Trial, Variety Release Trial, Clonal Evaluation, genetic_gain_trial, storage_trial, heterosis_trial, health_status_trial, grafting_trial, Screen House, Seed Multiplication, crossing_block_trial, Specialty Trial)
trial_stock_type (The type of stocks that are being evaluated in the trial. Can be either 'accession', 'cross', or 'family_name'. When not provided, 'accession' is used as the default)
plot_width (plot width in meters)
plot_length (plot length in meters)
field_size (field size in hectares)
planting_date (Date of Planting in YYYY-MM-DD format)
transplanting_date(The transplanting_date of the trial was conducted. Date in YYYY-MM-DD format)
harvest_date (Date of Harvest in YYYY-MM-DD format)
is_a_control (type 1 in this field if the plot is a control, otherwise 0 or leave blank. generally you will have accessions that are controls, so you should indicate the plots that that accession is in as a control.)
rep_number (replicate number, must be numeric)
range_number (range number. often synonymous with col_number, must be numeric)
row_number (row number. if the field is a grid, this represents the y coordinate, numeric, required for field map generation.)
col_number (column number. if the field is a grid, this represents the x coordinate. sometimes called range_number, numeric, required for field map generation.)
seedlot_name (the seedlot from where the planted seed originated. must exist in the database)
num_seed_per_plot (number seeds per plot. seed is transferred from seedlot mentioned in seedlot_name. numeric)
weight_gram_seed_per_plot (weight in gram of seeds in plot. seed is transferred from seedlot mentioned in seedlot name. numeric)
entry_number (a trial-level entry number assigned to the stock. Numeric)

Treatments:

treatment columns (additional column(s) that specify the name of a treatment (e.g. inoculated, drought, etc). the value for each plot should be 1 if the treatment was applied or empty if not applied.)

Trials may be uploaded using any of the supported file types: MS Excel (.xls or .xlsx), comma-separated file (.csv), tab-delimited file (.txt or .tsv), or semicolon-separated file (.ssv).

Optional columns may be left out, if not used in your data.

Header:
The first row (header) should contain the following:

trial_name	breeding_program	location	year	transplanting_date	planting_date	harvest_date	design_type	description	trial_type	plot_width	plot_length	field_size

Required Fields:

trial_name: the name of the trial (must already exist in the database)

Optional values:

new_trial_name (A new name for the trial, must not already exist in the database)
breeding_program (The name of breeding program that managed the trial, must exist in the database.)
location (The name or abbreviation of the location where the trial was held, must exist in the database.)
year (The year the trial was held.)
transplanting_date (The transplanting_date of the trial was conducted. Date in YYYY-MM-DD format or 'remove' to remove the date)
planting_date (Date of Planting in YYYY-MM-DD format or 'remove' to remove the date)
harvest_date (Date of Harvest in YYYY-MM-DD format or 'remove' to remove the date)
design_type (The shorthand for the design type, must exist in the database. Possible values include CRD (Completely Randomized Design), RCBD (Randomized Complete Block Design), RRC (Resolvable Row-Column), DRRC (Doubly-Resolvable Row-Column), URDD (Un-Replicated Diagonal Design), ARC (Augmented Row-Column), Alpha (Alpha Lattice Design), Lattice (Lattice Design), Augmented (Augmented Design), MAD (Modified Augmented Design), greenhouse (undesigned Nursery/Greenhouse), splitplot (Split Plot), p-rep (Partially Replicated), Westcott (Westcott Design))
description (Additional text with any other relevant information about the trial.)
trial_type (The name of the trial type, must exist in the database. Possible values include Seedling Nursery, phenotyping_trial, Advanced Yield Trial, Preliminary Yield Trial, Uniform Yield Trial, Variety Release Trial, Clonal Evaluation, genetic_gain_trial, storage_trial, heterosis_trial, health_status_trial, grafting_trial, Screen House, Seed Multiplication, crossing_block_trial, Specialty Trial)
plot_width (plot width in meters)
plot_length (plot length in meters)
field_size (field size in hectares)

Trial Metadata may be uploaded using any of the supported file types: MS Excel (.xls or .xlsx), comma-separated file (.csv), tab-delimited file (.txt or .tsv), or semicolon-separated file (.ssv).

Optional columns may be left out, if not used in your data.

Background:

Partially replicated designs have some treatments that are unreplicated and rely on replicated treatments to make the trial analysable. The design were described in Cullis et al. (2006). It is recommended that at least 20% of the experimental units are occupied by replicated treatments. The aim of these experiments is usually to select promising treatments from a set of replicated and unreplicated test treatments, with check and quality standard treatments providing the necessary replication overall to give a valid experiment. DiGGer (Coombes, 2002) was used to implement this design. DiGGer is a flexible tool for creating experimental designs that are efficient for specified blocking and correlation patterns. DiGGer package (http://www.austatgen.org/files/software/downloads) is an add-on for the statistical computing language and environment R (R Development Core Team, 2009).

Design Parameters:

The parameters will consider a sample partially replicated design trial with 200 unreplicated accessions, 119 accessions replicated 4 times, 26 rows in design, 26 columns in design, bock sequence of 13 by 2 (13, 2) i.e 2 blocks with each having 13 rows; sub-block sequence of block of 13 by 1 (13, 1) i.e 1 sub-block with each having 13 rows in each block.

List of Unreplicated Accession: You're expected to provide the list of unreplicated accessions in this selectbox. E.g. is a list of 200 accessions.
List of Replicated Accession: List of replicated accessions should be provided in this selectbox. E.g. is a list of 119 accessions.
Number of rows in design: Provide the number of rows you want to have in the design. E.g. 26 number of rows.
Number of Columns in Design: Provide the number of columns you want to have in the design. E.g. 26 number of columns.
Number of Times Replicated Accessions are Replicated: Provide the number of times you want the replicated accessions to be replicated. E.g. 4
Block Sequence: The block sequence should reflect the blocking structure of your design. E.g. (13, 2), meaning the design has 2 blocks and each block has 13 rows.
Sub-block Sequence: The sub-block sequence should reflect the sub-blocking structure of your design. E.g. (13, 1), meaning the design has 1 sub-block (column) and each sub-block has 13 rows.

NOTE:

The product of the number of rows and columns in the design should equal the total number of plots. The sum of the unreplicated accessions and the replicated accessions (given the number of times it was replicated) should equal the total number of plots.: The product of the number of rows and columns in the design should equal the total number of plots.; The sum of the unreplicated accessions and the replicated accessions (given the number of times it was replicated) should equal the total number of plots.

Intro
Data Type
Genotyping Project
Genotyping Protocol
Genotype Info
Confirm
Complete

This workflow will guide you through uploading genotypes into the database

Select a genotyping project on the next screen. This project can represent a series of genotyping plates sent to a genotyping facilty.

Ideally the sample names in your VCF file will match sample names in genotyping plates in the database; however, the sample names in your file can also match accession names in the database.

Curently we support the VCF format, the Tassel HDF5 format, the Intertek CSV format, KASP data and SSR data for upload.

If you are uploading many files that used the same genotyping protocol, you can do so, and the database will ensure that the marker information is consistent across the genotyping data (e.g. the same reference, alternate, position, etc.).
Select the type of genotyping data being uploaded

Type of genotyping data:

Select the genotyping project or create a new one. A genotyping project is a specific genotyping event. You can have many genotyping projects under the same genotyping protocol to indicate that those genotyping events used the same markers.

Select	Genotyping Project Name	Description	Breeding program	Year	Location	Genotyping Facility

Provide info about the genotyping protocol used. The genotyping protocol represents a specific instance of how genotypes were called for a set of markers in a genotyping platform. Many genotyping projects can use the same genotyping protocol.

Select	Protocol Name	Header Description	Number of Markers	Protocol Description	Reference Genome	Species	Sample Unit	Create Date

Genotyping Protocol Name:

Genotyping Protocol Reference Genome:

Species:

Assay Type

Description:

Choose Sample Unit:

   Exported Tissue Sample Name: The sample names in your VCF are tissue_sample_names that already exist in genotyping plates (e.g. 96 well plates) or sampling trials in the database. The sample names in your VCF file can be the tissue_sample_name triple pipe joined to the accession_name (e.g. tissue_sample_name|||accession_name) or just simply the tissue_sample_name corresponding to the genotyping plate well or sampling trial sample. This is the recommended format.

   Accession: The sample names are of accession names

   Mixed Stocks: The sample names are a mix of accession names or plot names or sample names or other stock names. This is not recommended because it will lead to messy sample metadata.

Location of Data Generation:

Exported Tissue Sample Names Include Numbers Generated by Genotyping Facility (e.g. sample_name:IGD1001:09):
The generated number is separated from the tissue sample name in the database by a ':' separating character.

Provide genotype information

Type of Genotype Data:

Ignore any possible warnings and upload genotypes?:

File format information
VCF format

Select VCF File:

File format information
VCF format

Select Tassel HDF5 (.h5) File:

File format information
Intertek format

Select Intertek SNP Result Grid File:

Select Intertek SNP Information File:

File format information
KASP data format

Select KASP Marker Information File (csv):

Select KASP Result File (csv):

File format information
SSR format

Select SSR File:

Finalize and submit your genotyping data

Add these missing stocks as new accessions?:
Complete! Your genotyping data was saved in the database.

The genotyping data was saved successfully

Complete!

This is for uploading VCF genotype data.
VCF is a tab separated format. If your VCF is very large (greater than 10GB), please consider converting it to an HDF5 (.h5) file using Tassel, and uploading the HDF5 formatted file instead.
Header:
The first row (header) must contain the following fields, followed by all genotyped sample names:

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Sample names...

Required fields:

#CHROM (chromosome: An identifier from the reference genome pointing to a contig in the assembly file (cf. the ##assembly line in the header). All entries for a specific CHROM should form a contiguous block within the VCF file. The colon symbol (:) must be absent from all chromosome names to avoid parsing errors when dealing with breakends. (String, no white-space permitted, Required))
POS (position: The reference position, with the 1st base having position 1. Positions are sorted numerically, in increasing order, within each reference sequence CHROM. It is permitted to have multiple records with the same POS. Telomeres are indicated by using positions 0 or N+1, where N is the length of the corresponding chromosome or contig. (Integer, Required) )
ID ( identifier: Semi-colon separated list of unique identifiers where available. If this is a dbSNP variant it is encouraged to use the rs number(s). No identifier should be present in more than one data record. If there is no identifier available, then the missing value should be used. (String, no white-space or semi-colons permitted) )
REF (reference base(s): Each base must be one of A,C,G,T,N (case insensitive). Multiple bases are permitted. The value in the POS field refers to the position of the first base in the String. For simple insertions and deletions in which either the REF or one of the ALT alleles would otherwise be null/empty, the REF and ALT Strings must include the base before the event (which must be reflected in the POS field), unless the event occurs at position 1 on the contig in which case it must include the base after the event; this padding base is not required (although it is permitted) for e.g. complex substitutions or other events where all alleles have at least one base represented in their Strings. If any of the ALT alleles is a symbolic allele then the padding base is required and POS denotes the coordinate of the base preceding the polymorphism. Tools processing VCF files are not required to preserve case in the allele Strings. (String, Required) )
ALT (alternate base(s): Comma separated list of alternate non-reference alleles. These alleles do not have to be called in any of the samples. Options are base Strings made up of the bases A,C,G,T,N,*, (case insensitive) or a breakend replacement string as described in the section on breakends. The '*' allele is reserved to indicate that the allele is missing due to a upstream deletion. If there are no alternative alleles, then the missing value should be used. Tools processing VCF files are not required to preserve case in the allele String, except for IDs, which are case sensitive. (String; no whitespace, commas, or angle-brackets are permitted in the ID String itself) )
QUAL (quality: Phred-scaled quality score for the assertion made in ALT. i.e. -10log10 prob(call in ALT is wrong). If ALT is '.' (no variant) then this is -10log10 prob(variant), and if ALT is not '.' this is -10log10 prob(no variant). If unknown, the missing value should be specified. (Numeric) )
FILTER (filter status: PASS if this position has passed all filters, i.e. a call is made at this position. Otherwise, if the site has not passed all filters, a semicolon-separated list of codes for filters that fail. e.g. "q10;s50" might indicate that at this site the quality is below 10 and the number of samples with data is below 50% of the total number of samples. "0" is reserved and should not be used as a filter String. If filters have not been applied, then this field should be set to the missing value. (String, no white-space or semi-colons permitted) )
INFO (additional information: (String, no white-space, semi-colons, or equals-signs permitted; commas are permitted only as delimiters for lists of values) INFO fields are encoded as a semicolon-separated series of short keys with optional values in the format: key=data[,data]. Arbitrary keys are permitted, although the following sub-fields are reserved (albeit optional):

AA : ancestral allele
AC : allele count in genotypes, for each ALT allele, in the same order as listed
AF : allele frequency for each ALT allele in the same order as listed: use this when estimated from primary data, not called genotypes
AN : total number of alleles in called genotypes
BQ : RMS base quality at this position
CIGAR : cigar string describing how to align an alternate allele to the reference allele
DB : dbSNP membership
DP : combined depth across samples, e.g. DP=154
END : end position of the variant described in this record (for use with symbolic alleles)
H2 : membership in hapmap2
H3 : membership in hapmap3
MQ : RMS mapping quality, e.g. MQ=52
MQ0 : Number of MAPQ == 0 reads covering this record
NS : Number of samples with data
SB : strand bias at this position
SOMATIC : indicates that the record is a somatic mutation, for cancer genomics
VALIDATED : validated by follow-up experiment
1000G : membership in 1000 Genomes

FORMAT (A format field is given specifying the data types and order (colon-separated alphanumeric String). This is followed by one field per sample, with the colon-separated data in this field corresponding to the types specified in the format. The first sub-field must always be the genotype (GT) if it is present. There are no required sub-fields. As with the INFO field, there are several common, reserved keywords that are standards across the community:
- GT : genotype, encoded as allele values separated by either of / or |. The allele values are 0 for the reference allele (what is in the REF field), 1 for the first allele listed in ALT, 2 for the second allele list in ALT and so on. For diploid calls examples could be 0/1, 1 | 0, or 1/2, etc. For haploid calls, e.g. on Y, male nonpseudoautosomal X, or mitochondrion, only one allele value should be given; a triploid call might look like 0/0/1. If a call cannot be made for a sample at a given locus, '.' should be specified for each missing allele in the GT field (for example './.' for a diploid genotype and '.' for haploid genotype). The meanings of the separators are as follows (see the PS field below for more details on incorporating phasing information into the genotypes):
- DP : read depth at this position for this sample (Integer)
- FT : sample genotype filter indicating if this genotype was "called" (similar in concept to the FILTER field). Again, use PASS to indicate that all filters have been passed, a semi-colon separated list of codes for filters that fail, or '.' to indicate that filters have not been applied. These values should be described in the metainformation in the same way as FILTERs (String, no white-space or semi-colons permitted)
- GL : genotype likelihoods comprised of comma separated floating point log10-scaled likelihoods for all possible genotypes given the set of alleles defined in the REF and ALT fields. In presence of the GT field the same ploidy is expected and the canonical order is used; without GT field, diploidy is assumed. If A is the allele in REF and B,C,... are the alleles as ordered in ALT, the ordering of genotypes for the likelihoods is given by: F(j/k) = (k*(k+1)/2)+j. In other words, for biallelic sites the ordering is: AA,AB,BB; for triallelic sites the ordering is: AA,AB,BB,AC,BC,CC, etc. For example: GT:GL 0/1:-323.03,-99.29,-802.53 (Floats)
- GLE : genotype likelihoods of heterogeneous ploidy, used in presence of uncertain copy number. For example: GLE=0:-75.22,1:-223.42,0/0:-323.03,1/0:-99.29,1/1:-802.53 (String)
- PL : the phred-scaled genotype likelihoods rounded to the closest integer (and otherwise defined precisely as the GL field) (Integers)
- GP : the phred-scaled genotype posterior probabilities (and otherwise defined precisely as the GL field); intended to store imputed genotype probabilities (Floats)
- GQ : conditional genotype quality, encoded as a phred quality -10log10 p(genotype call is wrong, conditioned on the site's being variant) (Integer)
- HQ : haplotype qualities, two comma separated phred qualities (Integers)
- PS : phase set. A phase set is defined as a set of phased genotypes to which this genotype belongs. Phased genotypes for an individual that are on the same chromosome and have the same PS value are in the same phased set. A phase set specifies multi-marker haplotypes for the phased genotypes in the set. All phased genotypes that do not contain a PS subfield are assumed to belong to the same phased set. If the genotype in the GT field is unphased, the corresponding PS field is ignored. The recommended convention is to use the position of the first variant in the set as the PS identifier (although this is not required). (Non-negative 32-bit Integer)
- PQ : phasing quality, the phred-scaled probability that alleles are ordered incorrectly in a heterozygote (against all other members in the phase set). We note that we have not yet included the specific measure for precisely defining "phasing quality"; our intention for now is simply to reserve the PQ tag for future use as a measure of phasing quality. (Integer)
- EC : comma separated list of expected alternate allele counts for each alternate allele in the same order as listed in the ALT field (typically used in association analyses) (Integers)
- MQ : RMS mapping quality, similar to the version in the INFO field. (Integer)
If any of the fields is missing, it is replaced with the missing value. For example if the FORMAT is GT:GQ:DP:HQ then 0 | 0 : . : 23 : 23, 34 indicates that GQ is missing. Trailing fields can be dropped (with the exception of the GT field, which should always be present if specified in the FORMAT field). )

This is for uploading Intertek genotype data.
Please use csv formatted files

For Intertek SNP Result Grid File:

The header must be:

SampleName.LabID	All Marker Names In Separate Columns (e.g. marker name = S12_7926132)

The SampleName.LabID column should contain the sample name (exported_tissue_sample_name or accession_name) and it must exist in the database already

For Intertek SNP Information File:

The header must be:

IntertekSNPID	CustomerSNPID	Reference	Alternate	Chromosome	Position	Optional: additional marker info can be included. Please see below.

Optional columns: You can include additional marker infomation by selecting one or more column headers listed below. Please add the selected column(s) after "Position" column.

Quality
Filter
Info
Format
Sequence

SSR marker info may be uploaded in an Excel file (.xls or .xlsx)
Header:
The first row (header) must contain the following fields:

marker_name	forward_primer	reverse_primer	annealing_temperature	product_sizes	sequence_motif	sequence_source	linkage_group

Required columns:

marker_name
forward_primer
reverse_primer
annealing_temperature
product_sizes

Optional columns (required in the header, but value may be left blank)

sequence_motif
sequence_source
linkage_group

SSR data may be uploaded in an Excel file (.xls or .xlsx)
Example of SSR Data Spreadsheet:

sample_name	s01	s01	s01	s02	s02	s02
	139	170	194	203	229	290
sample_A	1	0	0	0	1	1
sample_B	0	0	0	1	0	0
sample_C	0	1	1	0	1	0

Column Info:

s01 and s02 are marker names.
139, 170, 194 are product sizes generated by marker s01 and 203,229,290 are product sizes generated by marker s02.
sample_A, sample_B, sample_C are accession names.
"1" indicates the presence of PCR product.
"0" indicates the absence of PCR product.

This is for uploading KASP genotype data.
Please use csv formatted files

For KASP Marker Information File:

The header must be:

MarkerName	Xallele	Yallele	Chromosome	Position	Optional: additional marker info can be included. Please see below.

Note: For dosage calculation, Xallele is used as reference allele (0) and Yallele is used as alternative allele (1).
Optional columns: You can include additional marker information by selecting one or more column headers listed below. Please add the selected column(s) after "Position" column.

Quality
Filter
Info
Format
Sequence
FacilityMarkerName: if you are uploading genotyping data by using facility marker names, please include these names in the KASP marker information file using "FacilityMarkerName" header

For KASP Result File:
Note: If your genotyping facility assigned facility marker names and facility sample names for the genotyping data generated, you have an option to directly use these facility names for uploading. After uploaded into database, the genotyping data will be automatically linked to the original marker names and sample names.

If you are uploading genotyping data using your marker names and sample names, the header must be:

MarkerName

SampleName

SNPcall

Xvalue

Yvalue

Required columns:

MarkerName: Must exist in the marker information file. If you are uploading genotyping data using previously stored protocol, marker names must exist in the selected protocol.
SampleName: Must exist in the database as uniquenames.
SNPcall: Allele separated by ":" (for example A:G).
Xvalue: raw data of X.
Yvalue: raw data of Y.

If you are uploading genotyping data using facility marker names and facility sample names, the header must be:

FacilityMarkerName	FacilitySampleName	SNPcall	Xvalue	Yvalue

Required columns:

FacilityMarkerName: Must exist in the marker information file.
FacilitySampleName: Must exist in the database. You can create a link between each sample name and facility sample name by including facility sample name during uploading genotyping plates
SNPcall: Allele separated by ":" (for example A:G).
Xvalue: raw data of X.
Yvalue: raw data of Y.

This is for uploading a pre-existing genotyping plate layout.
File must be Excel file (.xls or .xlsx)
Header:
The first row (header) must contain the following:

date	sample_id	well_A01	row	column	source_observation_unit_name	ncbi_taxonomy_id	dna_person	notes	tissue_type	extraction	concentration	volume	is_blank

Optional column: In addition to sample ids, you can add facility identifiers in the last column with the header: "facility_identifier".

Required fields:

date (should be YYYY-MM-DD)
sample_id (the unique identifier for the sample in the well)
well_A01 (the position of the sample in the plate e.q. A10)
row (the row position of the sample in the plate e.g. A)
column (the column position of the sample in the plate e.g. 10)
source_observation_unit_name (must exist in the database. the identifier of the origin material. in order of most desirable identifier to least desirable identifier that can be used here: tissue sample name, plant name, plot name, accession name. For blank wells, you can write BLANK here and place a 1 in the is_blank column also.)
tissue_type (must be either leaf, root, stem, seed, fruit or tuber)

Optional fields:

ncbi_taxonomy_id (NCBI taxonomy identifier)
dna_person (the name of the person who prepared the well)
notes (any additional notes on the well)
extraction (free-text for the extraction method e.g. CTAB)
concentration (concentration in ng/ul)
volume (volume in ul)
is_blank (indicates if well is blank. write 1 if blank, otherwise leave empty.)
facility_identifier (if you would like to include facility identifiers in your genotyping plate layout, you can add facility identifiers in the last column with the header "facility_identifier")

This is for uploading a Default Coordinate Android Application exported plate layout.
File must be a CSV file (.csv)
(Excel format not supported)

Header:
The first row (header) must contain the following:

date	plate_id	plate_name	sample_id	well_A01	well_01A	tissue_id	dna_person	notes	tissue_type	extraction

Optional column: In addition to sample ids, you can add facility identifiers in the last column with the header: "facility_identifier".

Required fields:

date (should be YYYY-MM-DD)
plate_id (an identifier for a grouping of plates. called "Genotyping Project Name" in genotyping plate submission form. e.g. NextGenCassava)
plate_name (the unique name for the individual plate. called "Plate ID" in genotyping plate submission form. e.g. 18DNA00001)
sample_id (the unique identifier for the sample in the well. e.g. 18DNA00001_A01)
well_A01 (the position of the sample in the plate in this format A01)
well_01A (the position of the sample in the plate in this format 01A)
tissue_id (the identifier of the origin material. in order of most desirable identifier to least desirable identifier that can be used here: tissue sample name, plant name, plot name, accession name. this can also say 'BLANK' to indicate a blank well.)
dna_person (the name of the person who plated the individual sample. can be any name.)
tissue_type (must be either leaf, root, or stem)

Optional fields:

notes (any additional notes on the well)
extraction (free-text for the extraction method e.g. CTAB)
facility_identifier (if you would like to include facility identifiers in your genotyping plate layout, you can add facility identifiers in the last column with the header "facility_identifier")

This is for uploading a Custom Coordinate Android Application exported plate layout.
File must be a CSV file (.csv)
(Excel format not supported)

Header:
Note that tissue type will be set to 'leaf' if you use this upload type, since tissue type is not provided in the upload and tissue type is required for DaRT.

The first row (header) must contain the following:

Value	Column	Row	Identification	Person	Date

Optional column: In addition to sample ids, you can add facility identifiers in the last column with the header: "Facility Identifier".

Required fields:

Value (the identifier of the origin material. e.g. 2018MyPlant0001. in order of most desirable identifier to least desirable identifier that can be used here: tissue sample name, plant name, plot name, accession name. This can also say 'exclude' to indicate a BLANK)
Column (the column position of the sample e.g. 10)
Row (the row position of the sample e.g. A)
Identification (free text)
Person (the name of the person who plated the individual sample. can be any name.)
Date (should be YYYY-MM-DD)

Optional field:

Facility Identifier (if you would like to include facility identifiers in your genotyping plate layout, you can add facility identifiers in the last column with the header "Facility Identifier")

Intro
File format
Upload inventory
Fix missing seedlots problem
Try submitting inventory again

What is a seedlot inventory?
- Seedlots represent physical seed in packets.
- This seed can be from crosses or for named accessions.
- Seedlots can have a specific location, box, weight(g), and count.
- Seedlots can belong to breeding programs and organizations.
- Seedlots can be used in trials (e.g. they were planted in a plot) and they can be harvested from a plot or plant (e.g. a cross was performed and seeds were collected.)
- A seedlot inventory consists of giving a location and current weight(g) to your seedlots. The seedlot name is the unique identifier for each seedlot and so should be encoded in a barcode on each seedlot packet.
- You can use the "Inventory" Android Application to scan seedlot barcodes and record weight. If you prefer you can create your own CSV file and upload that, if you do not want to use the Inventory Application. For info about the format of the file to upload, go to the next tab.
- It is also possible to manually enter a transaction by going to the seedlot detail page and clicking "Add New Transaction".
Make sure you are collecting seedlot inventory in the following format

The "Seed Inventory" Android Application will export this same exact format by default.
Select your file and upload seedlot inventory

Upload File (.csv):
Fixing the missing seedlot(s) problem
- Seedlots must exist in the database prior to updating or adding inventory. The reason for this is that the inventory does not give information about the content (a named accession or a cross name) and this information is required for a seedlot to exist in the database. We also want to be careful about adding new seedlots into the database because we do not want data to be incorrectly linked to duplicates.
- When adding seedlots into the database, you can upload an Excel file or you can add seedlots one at a time.
Seedlot Inventory Upload Error Messages
Submit your inventory again. You should have corrected all errors by now, but if not please take a look at the errors in the red box below. You can continue to modify your file and then click Upload until it works.

There exist these problems in your file:

Finished! Your seedlot inventory is in the database

The seedlot inventory file was uploaded successfully

You may want to proceed to the seedlot detail page(s) for the seedlot(s) you just updated.
You can print barcodes for the seedlots.

Finished! Your seedlot inventory is in the database

The seedlot inventory file was uploaded successfully

You may want to proceed to the seedlot detail page(s) for the seedlot(s) you just updated.
You can print barcodes for the seedlots.

Seedlots may be uploaded in a CSV file (.csv)
(Excel .xls and .xlsx format not supported)

Header:
The first row (header) should contain the following:

box_id	seed_id	inventory_date	inventory_person	weight_gram

Required fields:

box_id (the name of the box that the seedlot is in. also called box_name.)
seed_id (unique identifier for the seedlot. must exist in the database. also called seedlot_name)
inventory_date (a timestamp for when the seedlot was inventoried)
inventory_person (the name of the person doing the inventory. can be any name. also called operator_name)
weight_gram (the weight in grams of the seedlot)

Intro
What seedlots do you have?
File format
Upload seedlots
Fix errors in file
Try submitting seedlots again

What are seedlots?
- Seedlots represent physical plant materials in packets/containers.
- Plant material in a seedlot can be seed, root, clone, plant, tissue culture or gametophype.
- If you would like to set a default material type for seedlots, please contact us.
- These plant materials can be from crosses or for named accessions.
- Seedlots can have a specific location, box, weight_gram, and count.
- Seedlots can belong to breeding programs and organizations.
- Seedlots can be used in trials (e.g. they were planted in a plot) and they can be harvested from a plot or plant (e.g. a cross was performed and seeds were collected.)
Seedlots fall into two categories

Select One:
Make sure your file matches the correct file format
Provide basic information about the seedlots and upload your file

Material Type:

Breeding Program:

Location of seedlot storage:

Organization Name:

Upload File:

Upload File:
Fix all errors in your file
- Accessions must exist in the database prior to adding seedlots of them. The reason for this is that an accession can be exist in many seedlots and therefore exists as a separate entity in the database. We also want to be careful about adding new accessions into the database because we do not want incorrectly duplicated data.
- When adding accessions into the database, you can use either a list of accessions or an Excel file.
- Crosses must exist in the database before adding your seed lots. The reason for this is that a cross can produce many seed lots and so the cross must exists as a separate entity in the database. We also want to be careful about adding new crosses into the database because we do not want data to be incorrectly linked to duplicates.
- When adding crosses into the database, you can upload an Excel file or you can add seedlots one at a time.
Seedlot Upload Error Messages
Submit your seedlots again. You should have corrected all errors by now, but if not please take a look at the errors in the red box below. You can continue to modify your file and then click Upload until it works.

There exist these problems in your file:

Finished! Your seedlots are now in the database

The seedlot file was uploaded successfully

You may want to proceed to the seedlot detail page(s) for the seedlot(s) you just created.
You can print barcodes for the seedlots.

Finished! Your seedlots are now in the database

The seedlot file was uploaded successfully

You may want to proceed to the seedlot detail page(s) for the seedlot(s) you just created.
You can print barcodes for the seedlots.

Header:
The first row (header) should contain the following:

seedlot_name	accession_name	operator_name	amount	weight_gram	description	box_name	quality	source

Required fields:

seedlot_name (must be unique)
accession_name (must exist in the database. the accession_name is the unique identifier for the named genotype)
operator_name (the name of the person who oversaw the inventory process. can be any name.)
amount (number of materials in seedlot. can be provided in conjunction with weight_gram. must provide a value for amount or weight_gram or both.)
AND/OR
weight_gram (weight in grams of seedlot. can be provided in conjunction with amount. must provide a value for amount or weight_gram or both.)
box_name (the box name that the plant material is located in. can be any name.)

Optional fields:

description (information about why this seedlot is being added)
quality (status of the seedlot, for example "ok", "moldy", "insect damage" etc.
source (an alternate source, such as a plot, subplot, or plant identifier from which the seed was collected)

Seedlots may be uploaded using any of the supported file types: MS Excel (.xls or .xlsx), comma-separated file (.csv), tab-delimited file (.txt or .tsv), or semicolon-separated file (.ssv).

Optional columns may be left out, if not used in your data.

Header:
The first row (header) should contain the following:

seedlot_name	cross_unique_id	operator_name	amount	weight_gram	description	box_name	quality

Required fields:

seedlot_name (must be unique)
cross_unique_id (must exist in the database. a cross_unique_id can represent a cross between accessions e.g. AxB, but a cross can also represent a cross between specific plots in the field if you have this information)
operator_name (the name of the person who oversaw the inventory process. can be any name.)
amount (number of materials in seedlot. can be provided in conjunction with weight_gram. must provide a value for amount or weight_gram or both.)
AND/OR
weight_gram (weight in grams of seedlot. can be provided in conjunction with amount. must provide a value for amount or weight_gram or both.)
box_name (the box name that the plant material is located in. can be any name.)

Optional fields:

description (information about why this seedlot is being added)
quality (brief description of quality, e.g., "ok", "moldy", "insect damage", etc)

Seedlots may be uploaded using any of the supported file types: MS Excel (.xls or .xlsx), comma-separated file (.csv), tab-delimited file (.txt or .tsv), or semicolon-separated file (.ssv).

Optional columns may be left out, if not used in your data.

Using Lists
Uploading a File

File format information
Spreadsheet format

Upload File:

Email Alert:

Use Fuzzy Search:

Note: Use the fuzzy search to match similar names to prevent uploading of duplicate accessions. Fuzzy searching is much slower than regular search. Only a curator can disable the fuzzy search.

Append Synonyms:

When checked, add synonyms of existing accession entries to the synonyms already stored in the database. When not checked, remove any existing synonyms of existing accession entries and store only the synonyms in the upload file.

Accessions may be uploaded using any of the supported file types: MS Excel (.xls or .xlsx), comma-separated file (.csv), tab-delimited file (.txt or .tsv), or semicolon-separated file (.ssv).

Optional columns may be left out, if not used in your data.

Header:
The first row (header) should contain the following:

accession_name	species_name	population_name	organization_name	synonym	description	PUI	accession number	acquisition date	biological status of accession code	country of origin	donor	donor PUI	donor institute	genome_structure	institute code	institute name	introgression_backcross_parent	introgression_chromosome	introgression_end_position_bp	introgression_map_version	introgression_parent	introgression_start_position_bp	location_code	ncbi_taxonomy_id	notes	organization	ploidy_level	product_profile	released_variety_name	seed source	state	transgenic	type of germplasm storage code	variety	variety_release_id	year_of_cloning

Comma Separated Fields:

The following fields can take comma-separated values to indicate there are several values for the accession: organization_name, synonym , PUI, accession number, acquisition date, biological status of accession code, country of origin, donor, donor PUI, donor institute, genome_structure, institute code, institute name, introgression_backcross_parent, introgression_chromosome, introgression_end_position_bp, introgression_map_version, introgression_parent, introgression_start_position_bp, location_code, ncbi_taxonomy_id, notes, organization, ploidy_level, product_profile, released_variety_name, seed source, state, transgenic, type of germplasm storage code, variety, variety_release_id, year_of_cloning

Required Fields:

accession_name (must be unique)
species_name (must exist in the database)

Optional Fields:

description - a free text description of the stock.
population_name (a population is a grouping of accessions. If the population already exists in the database, the accession will be added to it; otherwise, a new population will be created). Multiple populations can be specified, using the pipe symbol (|) as the separator (for example, pop1|pop2|pop3)
organization_name (the name(s) of the organization(s) which use this accession e.g. NARO,IITA)
synonym (an accession can be known by many names including local popular names. a synonym name can be used instead of the accession_name throughout the database; because of this, synonyms must themselves be unique. e.g. accession_synonym1,accession_synonym001)
PUI (no definition available)
accession number (no definition available)
acquisition date (no definition available)
biological status of accession code (no definition available)
country of origin (no definition available)
donor (no definition available)
donor PUI (no definition available)
donor institute (no definition available)
genome_structure (no definition available)
institute code (no definition available)
institute name (no definition available)
introgression_backcross_parent (no definition available)
introgression_chromosome (no definition available)
introgression_end_position_bp (no definition available)
introgression_map_version (no definition available)
introgression_parent (no definition available)
introgression_start_position_bp (no definition available)
location_code (no definition available)
ncbi_taxonomy_id (no definition available)
notes (no definition available)
organization (no definition available)
ploidy_level (no definition available)
product_profile (no definition available)
released_variety_name (no definition available)
seed source (no definition available)
state (no definition available)
transgenic (no definition available)
type of germplasm storage code (no definition available)
variety (no definition available)
variety_release_id (no definition available)
year_of_cloning (no definition available)

Accessions may be uploaded using any of the supported file types: MS Excel (.xls or .xlsx), comma-separated file (.csv), tab-delimited file (.txt or .tsv), or semicolon-separated file (.ssv).

Optional columns may be left out, if not used in your data.

Intro
Crossing experiment
Upload your crosses

Introduction
- Crosses can be of different types (biparental, self, open, backcross, sib, polycross, bulk, bulk_open, bulk_self, doubled_haploid, or dihaploid_induction)
- An individual cross can be linked to a female plot or plant, as well as a male plot or plant.
- A cross can have a number of properties associated to it, such as number of flowers, pollination date, etc.
- A cross can produce seed, which goes into a seedlot.
- A cross can ultimately produce progeny, which then become named accessions in the database.
Select a crossing experiment for your crosses
If you are uploading an Intercross file and using auto-generated cross unique IDs, please use manage Intercross section

Crossing experiments are for grouping crosses together. The grouping is most often done for crosses derived from the same field trial, the same year, or for crosses that have the same breeding objective.

You are uploading crosses for crossing experiment:

Enter basic information about the crosses and upload your file

File format information
Spreadsheet format

Upload File:

Crosses may be uploaded using any of the supported file types: MS Excel (.xls or .xlsx), comma-separated file (.csv), tab-delimited file (.txt or .tsv), or semicolon-separated file (.ssv).

Finished! Your crosses are now in the database

The crosses file was uploaded successfully

You may want to proceed to the cross detail page(s) for the cross(es) you just created.
You can print barcodes for the crosses.
You can add crossing information as it becomes available (e.g. number of seeds, progeny, etc).

Finished! Your crosses are now in the database

The crosses file was uploaded successfully

You may want to proceed to the cross detail page(s) for the cross(es) you just created.
You can print barcodes for the crosses.
You can add crossing information as it becomes available (e.g. number of seeds, progeny, etc).

Header:
To set up crosses in the database, please provide required information. The first row (header) must contain the following:

cross_unique_id

cross_combination

cross_type

female_parent

male_parent

Required columns:

cross_unique_id (must NOT exist in the database)
cross_combination (required in the header, but value for cross combination (e.g. female accession/male accession) may be left blank)
cross_type (must be one of the following: biparental, self, open, sib, polycross, backcross, bulk, bulk_open, bulk_self, doubled_haploid, dihaploid_induction)

biparental: An individual plant pollinated by another individual plant.
self: A self pollinated individual plant.
open: An individual plant pollinated by a group of plants or open pollinated (pollen may be from a group with known or unknown members).
backcross: An individual plant pollinated by one of its parents.
sib: Mating between individuals that have at least one parent in common. Generally between two individuals within the same plot.
polycross: Mating between individual female parent from a population and the corresponding male population.
bulk: A group of plants (usually a related family) pollinated by an individual plant (between a female population and a male accession).
bulk_open: A group of plants (usually a related family) that are pollinated by another group of plants or open pollinated (between a female population and a male population or unknown male parent).
bulk_self: A group of plants (usually a related family) that are self pollinated (each individual selfed, not combined pollen).
doubled_haploid: Plants derived from doubling the chromosome number of haploid tissue.
dihaploid_induction: Plants derived from reducing the chromosome set from 4 to 2.

female_parent: Female parent names must exist as uniquenames in the database, can be accession, plot, plant or population stock type.
male_parent: Required in the header, but value may be left blank for most cross types. Must be specified for biparental, sib, backcross, polycross and bulk cross types. When specified, male parent names must exist as uniquenames in the database, can be accession, plot, plant or population stock type.

Optional columns (additional parent info): You can add additional parent info after male_plant column by using one or more of these column headers.

objective
female_focus_trait
male_focus_trait
female_source_trial
male_source_trial

Additional cross information:

After cross unique ids are stored in the database, you can add field crossing data (e.g. pollination date, total number of flowers pollinated, total number of fruits set) or progenies to each cross unique id.
Field crossing data and progenies can be uploaded via links in crossing experiment detail page or can be added directly in each cross detail page.

Intro
Add a crossing experiment

What are crossing experiments?

Crossing experiments group crosses. The grouping can reflect crosses done in the same field trial, crosses in a breeding program in a given year, or crosses that have the same breeding objective. This grouping can be used to encapsulate all the crosses done in a crossing block field trial that you have saved in the database (e.g. in Manage Trials your crossing block will appear as a field trial with plots)
Enter basic information about the crossing experiment

Crossing Experiment Name:

Breeding Program:

Location of crossing experiment:

Year:

Description:

Finished! Your crossing experiment is now in the database

Crossing experiment was added successfully

You may want to proceed to the crossing experiment detail page you just created.
You can add or upload crosses into your crossing experiment as they become available.
You can add crossing information as it becomes available (e.g. number of seeds, progeny, etc).

Finished! Your crossing experiment is now in the database

Crossing experiment was added successfully

You may want to proceed to the crossing experiment detail page you just created.
You can add or upload crosses into your crossing experiment as they become available.
You can add crossing information as it becomes available (e.g. number of seeds, progeny, etc).

Accessions	Seedlots
Accessions		Breeding Program	Seedlot Name	Contents	Seedlot Location	Count	Weight(g)

Attribute	Value
Project Name:
Start Date:
End Date:
Event Type:
Event Description:
Event Web URL:

Notice

Before creating a new account, please check if you already have an account using the directory search.
A link will be emailed to you. Please click on it to activate the account.
All fields are required.

First Name:

Last Name:

Organization:

Username:

Username must be at least 7 characters long.

Password:

Password must be at least 7 characters long and different from your username.

Confirm Password:

Password must be at least 7 characters long and different from your username.

Email Address:

An email will be sent to this address requiring you to confirm its receipt to activate your account.

Add New Accessions for Progeny:	Number of progeny:
Use Prefix and/or Suffix:	Prefix: Suffix:

Cassava Genomes

Breeding programs

NextGenCassava Community

& Partners

SGN SlideShare

New to the database?

Which accessions will be in the field?

Which crosses will be in the field?

Which family names will be in the field?

Number of Plants:

Number of Columns (required):

Number of columns between two check columns (Optional):

Which seedlots will you grow in the field? This is optional and can be decided later. If you do not know exactly which seedlot packets you will be planting at this time, you can add this information on the Trial Detail Page after the trial has been saved in the database.

Which seedlots will you grow in the field?
This is optional and can be decided later. If you do not know exactly which seedlot packets you will be planting at this time, you can add this information on the Trial Detail Page after the trial has been saved in the database.