skip to main content

SRA Toolkit Documentation

SRA Toolkit Installation and Configuration Guide

Protected Data Usage Guide

Frequently used tools:

abi-dump: Convert SRA data into ABI format (csfasta / qual)

fastq-dump: Convert SRA data into fastq format

illumina-dump: Convert SRA data into Illumina native formats (qseq, etc.)

prefetch: Allows command-line downloading of SRA, dbGaP, and ADSP data

sam-dump: Convert SRA data to sam format

sff-dump: Convert SRA data to sff format

sra-stat: Generate statistics about SRA data (quality distribution, etc.)

sra-pileup: Generate pileup statistics on aligned SRA data

vdb-config: Display and modify VDB configuration information

vdb-dump: Output the native VDB format of SRA data.

vdb-encrypt: Encrypt non-SRA dbGaP data ("phenotype data")

vdb-decrypt: Decrypt non-SRA dbGaP data ("phenotype data")

vdb-validate: Validate the integrity of downloaded SRA data