Simplified Access to SRA Genomic Data within GATK

The NCBI Sequence Read Archive (SRA) is the primary sequence repository for NIH-funded high throughput sequencing activities, and the current 4.3 petabases of sequence of which 54% is open access without restriction. Computational access to SRA data, both public and controlled, is provided via the sra-toolkit, a software product developed by NCBI. It is freely available and runs in linux, mac and windows operating systems. Popular functions within the SRA toollkit include: fastq-dump to convert SRA data into FASTQ format; prefetch to transfer an SRA record to local disk in native format; sam-dump to write out SRA data in SAM format, and sra-pileup to generate pileup statistics for aligned SRA data, i.e. BAM submissions.

NCBI has further simplified access to SRA data by developing software extensions within the Broad Institute’s GATK genomic sequence analysis package. This presentation will demonstrate the installation and execution steps for [aligning reads and] calling variants in Glycene max without the burden of pre-fetching accession sequences or genome reference.