SRA Toolkit protocols

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



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  • person_outline Rasko Leinonen <>

Additional information

Publication for Short Read Archive Toolkit

SRA Toolkit IN pipelines

PMCID: 5802526
PMID: 29317610
DOI: 10.1038/s41398-017-0053-y

[…] performed on two donor samples, for which both neun-positive and neun-negative sorted cell populations were available. sra files were converted to fastq files using fastq-dump, part of the sra toolkit available from ncbi ( fastq files were then processed as previously described12. briefly, data were aligned using bowtie213, and converted to bam, […]

PMCID: 5834250
PMID: 29541392
DOI: 10.18632/oncotarget.24228

[…] 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: 5837560
PMID: 29504936
DOI: 10.7554/eLife.31989.020

[…] script. the directionality of the downstream genes was obtained using yeast net-seq data from (marquardt et al., 2014) (accession gse55982). the raw reads were extracted from sra archives using sra toolkit v2.6.3, quality and adapter trimming was performed using trim galore v0.4.3 and alignment to the yeast genome was done using bowtie2 (--very-sensitive-local mode). the sam files […]

PMCID: 5888714
PMID: 29425311
DOI: 10.1093/gbe/evy032

[…] rna-seq data set srr3135045 (von heckel et al. 2016) for zambian d. melanogaster from the ncbi sra (; last accessed february 15, 2018). raw reads were downloaded with sra toolkit (v. 2.8.0). then we trimmed this data using trimmomatic (v. 0.32) and made quality control using fastqc (v. 0.10.1). transcriptome was mapped to d. melanogaster reference genome (dm3) […]

PMCID: 5457141
PMID: 28489004
DOI: 10.7554/eLife.23253.044

[…] of gene lists were performed using the go-elite (zambon et al., 2012)., to examine gene expression in arg in human and mouse neocortex, fastq files were obtained using the fastq-dump program of the sra toolkit from the gene expression omnibus, under the accession numbers gse30765, gse38805, gse65000, and gse66217. these datasets contained 13 human and 21 mouse rna-seq samples of the vz or arg. […]

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

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