SRA Toolkit

sratoolkit

A toolkit for using data in the INSDC Sequence Read Archives.

Runs as prefetch, fasterq-dump, vdb-config|macOS, Linux, Windows|github.com

Open form in Otty otty.toml

Command form

ai-draft · 2 tasks · 3 fields

Download one or more SRA run accessions with prefetch, resumable on failure. Only prefetch is covered; fasterq-dump and vdb-config have no form.

Opens the form; the finished command lands at your prompt, unrun

Run in Otty

otty gui sratoolkit

Download SRA accessions (prefetch)Example values, fixed in this page — nothing here reaches a terminal

Basic

Accessions*

string

Output directory

directory

TasksEach one presets the form for one job

Download accessions

accessionsoutput_dir

Download a large accession

accessionsmax_sizeoutput_dir

ParametersOnly these flags are editable in the form

Accessions

SRA run accessions such as SRR000001.
string · positional 0 · repeatable

Output directory

The last directory should be named after the accession.
path

-O

Maximum download size

Default limit is 20G. Suffixes k, m, g, t; u means unlimited.
string

--max-sizeu100g

SourcesEvery flag above is checked against these

wiki

$prefetch SRR000001 -O /path/to/be/used Make sure the last directory of /path/to/be/used is the accession itself. $prefetch SRR1951777 --max-size 420000000000 kilobytes (default): --max-size 10 == --max-size 10k : 10 kilobytes, megabytes: --max-size 10m : 10 megabytes, gigabytes: --max-size 10g : 10 gigabytes, terabytes: --max-size 10t : 10 terabytes, unlimi…

manual2026-10-27

github.com

Before it fills your prompt, Otty checks the installed prefetch against its version. A form that does not match your version is not offered.