SRA Toolkit specifications


Unique identifier OMICS_03771
Name SRA Toolkit
Alternative name Short Read Archive Toolkit
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format SRA
Output format FASTA, FASTQ, SFF, SAM, BAM
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 2.8.2-1
Stability Stable
Maintained Yes



Add your version


  • person_outline Rasko Leinonen <>

Additional information

SRA Toolkit article

SRA Toolkit citations

PMCID: 5834250

[…] 220 samples were the only publicly-available samples annotated as brain-specific in the sra database upon their download on september 16, 2016. these datasets were processed into a gem using the sra toolkit v2.5.2 [12], trimmomatic v0.33 [17], hisat2-2.0.1-beta [18], samtools v0.1.19 [19, 20], and cufflinks v2.2.1 [21]. the gencode v24 gff3 file, complete with scaffolds, assembly patches, […]

PMCID: 5789949

[…] assembly before being deposited into the nih’s dbgap database that has been made available through an investigator agreement (r.k.). we obtained the aligned sequences from dbgap using the nih’s sra-toolkit (version 2.5.4). the read sequences for the cfh (chromosome 1) and arms2 (chromosome 10) loci were processed using the samtools package ( to deduce unphased genotypes […]

PMCID: 5731800

[…] (lin28a) and srr531465 (lin28v5). the wormbig and wormsmall data sets from ref. 27 were transferred via personal communication. the sra files were downloaded and converted to fastq files using sra toolkit 2.5.2. fastqc determined the sequence quality and presence of adapters. bowtie2 indexes were created for hg19, mm10 and ce10 for human (h. sapiens), mouse (m. musculus), and worm (c. […]

PMCID: 5599659

[…] source of the rna-seq dataset along with several metrics resulting from the alignment of the reads to the reference genome. briefly, we downloaded the single end datasets in fastq format using the sra toolkit (fastq-dump command), and the paired end datasets were directly downloaded from ena. we ensured the quality of the aligned sequence reads to a minimum quality score of 20 for each sample […]

PMCID: 5632840

[…] plus cd28 stimulation (49) were retrieved from gene expression omnibus series accession numbers gsm2370626 (resting) and gsm2370628 (with 150-min cd3 plus cd28), converted from sra to fastq with the sra toolkit fastq-dump using the split-files option to obtain paired-end fastq files. reads were subsequently aligned to the hs37d5 release of the human genome using tophat, as in this study. […]

SRA Toolkit institution(s)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK

SRA Toolkit reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review SRA Toolkit