Proposed formats and databases for genomics data

[dlebauer]

(by Mike Gore and Elodie Gazave)

Genomic data have reached a high level of standardization in the scientific community. Below are the most widely accepted formats that are relevant to the data and analyses that will be generated in this project.

Today, all high-impact journals typically ask the author to deposit their genomic data in either or both of these databases before publication.

Overview of Genomics Pipeline

Details

Raw reads + quality scores

Raw reads + quality scores are stored in FASTQ format. FASTQ files can be manipulated for QC with FASTX-Toolkit

Reference genome assembly

Reference genome assembly (for alignment of reads or BLAST) is in FASTA format. FASTA files generally need indexing and formatting that can be done by aligners, BLAST, or other applications that provide built-in commands for this purpose.

Sequence alignment

Sequence alignments are in BAM format – in addition to the nucleotide sequence, the BAM format contains fields to describe mapping and read quality. BAM files are binary files but can be visualized with IGV. If needed, BAM can be converted in SAM (text file) with SAMtools

BAM is the preferred format for sra database (sequence read archive).

de novo sequence alignment

Not part of milestone, though some groups may wish to do this. Will implement if / when needed. Reference sequences will be 17x, (perhaps not enough for de novo alignment).

SNP and genotype variants

SNP and genotype variants are in VCF format. VCF contains all information about read mapping and SNP and genotype calling quality. VCF files are typically manipulated with vcftools

VCF format is also the format required by dbSNP, the largest public repository all SNPs.

Genomic coordinates

Genomic coordinates are given in a BED format – gives the start and end positions of a feature in the genome (for single nucleotides, start = end). http://www.ensembl.org/info/website/upload/bed.html BED files can be manipulated with bedtools

Genome annotations

Genome annotations are in GFF format GFF format contains genes and other genomic features. Allows “track” info for visualization http://useast.ensembl.org/info/website/upload/gff.html

Visualizing and annotating Genomes

Gbrowse is a comprehensive database + interactive web application for manipulating and displaying annotations on genomes.

Downstream

Analysis tools that all use SNP data (vcf) as input.

• TASSEL-GBS
• GAPIT
• MLMM
• R/qtl

Repository

Submit variant calls to Phytozome, has embedded Jbrowse

[nfahlgren]

I would replace Gbrowse (if we are hosting this ourselves in the Cat5 team) with Jbrowse (http://jbrowse.org/). It's Javascript-based, so it has a much more responsive interface. It's also a GMOD project and is meant to replace Gbrowse at some point. Phytozome has switched to it already. It's compatible with the same data formats as Gbrowse, so not much has to change.

[cjfields]

What @nfahlgren said. We're advocating people switch to (and support!) JBrowse when possible.

[dlebauer]

@egazave : how do you link this to downstream pipelines such as Tassel or GapIT? Can we also implement these?

Yes, we can link to downstream programs for GWAS. If we want to use GAPIT, I can share the python script I have to transform a vcf to GAPIT input format.

[dlebauer]

@egazave yes, please share the script. I've spoken with Alex Lipka who in
interested in helping us to integrate GapIT
On Thu, Dec 10, 2015 at 11:27 AM egazave notifications@github.com wrote:

Yes, we can link to downstream programs for GWAS. If we want to use GAPIT,
I can share the python script I have to transform a vcf to GAPIT input
format.

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#19 (comment)
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[dlebauer]

(from Geoff:) Phytozome holds the JGI sorghum reference genome so we should probably plan to submit the variant calls to them so it can be browsed as a “Population variation” track on JBrowse.