macOS
Homebrewverified · 100%
brew install sratoolkitprovider-native install command
brew / rank 3307
Install sratoolkit with Homebrew
Data tools for INSDC Sequence Read Archive. Version 3.4.1 via Homebrew; verified from local package data.
install
Additional install commands
overview
Package summary
Data tools for INSDC Sequence Read Archive
Project links
Commands and aliases
- abi-dump
- abi-dump.3
- abi-dump.3.4.1
- align-info
- align-info.3
- align-info.3.4.1
- check-corrupt
- check-corrupt.3
- check-corrupt.3.4.1
- fasterq-dump
- fasterq-dump-orig.3.4.1
- fasterq-dump.3
- fasterq-dump.3.4.1
- fastq-dump
- fastq-dump-orig.3.4.1
- fastq-dump.3
- fastq-dump.3.4.1
- illumina-dump
- illumina-dump.3
- illumina-dump.3.4.1
- kdbmeta
- kdbmeta.3
- kdbmeta.3.4.1
- ngs-pileup
- ngs-pileup.3
- ngs-pileup.3.4.1
- prefetch
- prefetch-orig.3.4.1
- prefetch.3
- prefetch.3.4.1
- rcexplain
- rcexplain.3
history
Project history and usage
SRA Toolkit is NCBI's command-line toolkit for working with data in the INSDC Sequence Read Archive. It is one of the standard bioinformatics packages that turns accession identifiers into local data files and converts SRA containers into FASTQ, FASTA, SAM, and related analysis formats.
Project history
The project is maintained in NCBI's `sra-tools` repository and organized around many small CLI tools, including `prefetch`, `fasterq-dump`, `fastq-dump`, `sam-dump`, `vdb-config`, `vdb-validate`, and related VDB utilities. Its release notes show long-running 2.x and 3.x maintenance, with changes covering download behavior, cloud access, build systems, and format conversion.
SRA Toolkit 3.0.1 reorganized the source tree so the end-user toolkit, internal tools, archive loaders, and test tools were separated into different tool categories. That change made explicit the distinction between the tools ordinary package users install and the broader internal machinery around NCBI's archive workflows.
Adoption history
The package metadata in this batch shows SRA Toolkit packaged by Homebrew and Nix, while NCBI's own wiki documents Linux, macOS, Windows, Docker, and cloud workflows. In practice, package managers carry it because reproducible sequencing workflows often need the same accession-download and FASTQ-conversion commands on laptops, workstations, clusters, and containers.
How it is used
Common usage centers on `prefetch` to download an accession and `fasterq-dump` to extract FASTQ or FASTA output. The official wiki recommends the `prefetch` plus `fasterq-dump` workflow, documents resumable downloads, validation with `vdb-validate`, local cache configuration with `vdb-config`, and scratch-space considerations for large conversions.
Configuration is a real part of SRA Toolkit usage. NCBI documents `vdb-config -i`, the user repository, remote-access settings, cloud identity reporting, and the `${HOME}/.ncbi/user-settings.mkfg` settings file used by containerized runs.
Why package nerds care
SRA Toolkit is package-nerd significant because it is a large scientific CLI suite with many executables, nontrivial runtime configuration, network access, cache behavior, and cloud credential paths. Packaging it well affects reproducible bioinformatics pipelines, HPC modules, container images, and users who expect `prefetch` and `fasterq-dump` to behave consistently across platforms.
Timeline
- 2021: Official wiki documented toolkit configuration with `vdb-config` and cache/user-repository settings.
- 2022: SRA Toolkit 3.0.1 removed the requirement for interactive configuration and reorganized repository tool categories.
- 2023: SRA Toolkit 3.0.5 added PacBio support and reference-sequence output features to `fasterq-dump`.
- 2024: SRA Toolkit 3.1.0 added SRA Lite-related `prefetch` behavior and AlmaLinux support.
- 2025: SRA Toolkit 3.2.x release notes continued maintenance of `prefetch`, `fasterq-dump`, and build behavior.
Related projects
- SRA Toolkit is tied to NCBI SRA, INSDC sequence archives, NCBI VDB, dbGaP controlled-access workflows, and cloud storage access patterns documented by NCBI.
Sources
security posture
Risk level: blue
broad file, network, media, or database tool signal.
Risk classifier
blue risk · medium confidence · tool
Why
- broad file, network, media, or database tool signal
Signals
- text:archive,encrypt,decrypt
Install behavior
- No Homebrew bottle metadata was recorded.
Recommended review
Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.
local files
Configuration and credential file locations
These source-backed paths show where this package keeps local settings or durable credentials. Automic Vault can use them as review targets for secret scanning, migration, and command approval.
Configuration files
Config paths the tool may read or write during local use.
- Unix
${HOME}/.ncbi/user-settings.mkfg
executables
Installed executables
| Command | Kind | Exposure | Note |
|---|---|---|---|
abi-dump | executable | indexed executable | Discovered from the local executable index. |
abi-dump.3 | executable | indexed executable | Discovered from the local executable index. |
abi-dump.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
align-info | executable | indexed executable | Discovered from the local executable index. |
align-info.3 | executable | indexed executable | Discovered from the local executable index. |
align-info.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
check-corrupt | executable | indexed executable | Discovered from the local executable index. |
check-corrupt.3 | executable | indexed executable | Discovered from the local executable index. |
check-corrupt.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
fasterq-dump | executable | indexed executable | Discovered from the local executable index. |
fasterq-dump-orig.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
fasterq-dump.3 | executable | indexed executable | Discovered from the local executable index. |
fasterq-dump.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
fastq-dump | executable | indexed executable | Discovered from the local executable index. |
fastq-dump-orig.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
fastq-dump.3 | executable | indexed executable | Discovered from the local executable index. |
fastq-dump.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
illumina-dump | executable | indexed executable | Discovered from the local executable index. |
illumina-dump.3 | executable | indexed executable | Discovered from the local executable index. |
illumina-dump.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
kdbmeta | executable | indexed executable | Discovered from the local executable index. |
kdbmeta.3 | executable | indexed executable | Discovered from the local executable index. |
kdbmeta.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
ngs-pileup | executable | indexed executable | Discovered from the local executable index. |
ngs-pileup.3 | executable | indexed executable | Discovered from the local executable index. |
ngs-pileup.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
prefetch | executable | indexed executable | Discovered from the local executable index. |
prefetch-orig.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
prefetch.3 | executable | indexed executable | Discovered from the local executable index. |
prefetch.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
rcexplain | executable | indexed executable | Discovered from the local executable index. |
rcexplain.3 | executable | indexed executable | Discovered from the local executable index. |
rcexplain.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
ref-variation | executable | indexed executable | Discovered from the local executable index. |
ref-variation.3 | executable | indexed executable | Discovered from the local executable index. |
ref-variation.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
sam-dump | executable | indexed executable | Discovered from the local executable index. |
sam-dump-orig.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
sam-dump.3 | executable | indexed executable | Discovered from the local executable index. |
sam-dump.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
sff-dump | executable | indexed executable | Discovered from the local executable index. |
sff-dump.3 | executable | indexed executable | Discovered from the local executable index. |
sff-dump.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
sra-info | executable | indexed executable | Discovered from the local executable index. |
sra-info.3 | executable | indexed executable | Discovered from the local executable index. |
sra-info.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
sra-pileup | executable | indexed executable | Discovered from the local executable index. |
sra-pileup-orig.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
sra-pileup.3 | executable | indexed executable | Discovered from the local executable index. |
sra-pileup.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
sra-search | executable | indexed executable | Discovered from the local executable index. |
sra-search.3 | executable | indexed executable | Discovered from the local executable index. |
sra-search.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
sra-stat | executable | indexed executable | Discovered from the local executable index. |
sra-stat.3 | executable | indexed executable | Discovered from the local executable index. |
sra-stat.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
srapath | executable | indexed executable | Discovered from the local executable index. |
srapath-orig.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
srapath.3 | executable | indexed executable | Discovered from the local executable index. |
srapath.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
sratools | executable | indexed executable | Discovered from the local executable index. |
sratools.3 | executable | indexed executable | Discovered from the local executable index. |
sratools.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
test-sra | executable | indexed executable | Discovered from the local executable index. |
test-sra.3 | executable | indexed executable | Discovered from the local executable index. |
test-sra.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
var-expand | executable | indexed executable | Discovered from the local executable index. |
var-expand.3 | executable | indexed executable | Discovered from the local executable index. |
var-expand.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
vdb-config | executable | indexed executable | Discovered from the local executable index. |
vdb-config.3 | executable | indexed executable | Discovered from the local executable index. |
vdb-config.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
vdb-decrypt | executable | indexed executable | Discovered from the local executable index. |
vdb-decrypt.3 | executable | indexed executable | Discovered from the local executable index. |
vdb-decrypt.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
vdb-dump | executable | indexed executable | Discovered from the local executable index. |
vdb-dump-orig.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
vdb-dump.3 | executable | indexed executable | Discovered from the local executable index. |
vdb-dump.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
vdb-encrypt | executable | indexed executable | Discovered from the local executable index. |
vdb-encrypt.3 | executable | indexed executable | Discovered from the local executable index. |
vdb-encrypt.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
vdb-validate | executable | indexed executable | Discovered from the local executable index. |
vdb-validate.3 | executable | indexed executable | Discovered from the local executable index. |
vdb-validate.3.4.1 | executable | indexed executable | Discovered from the local executable index. |
freshness
Version and freshness
These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.
page generated2026-08-03
manager version3.4.1
manager updated
local dataunknown
upstreamnot available
latest detectednot detected
- okNo freshness warnings were generated.
install metadata
Package metadata
| Package key | brew:sratoolkit |
|---|---|
| Version | 3.4.1 |
| Package manager | Homebrew |
| Homepage | https://github.com/ncbi/sra-tools |
| Repository | https://github.com/ncbi/sra-tools |
| Bottle | not recorded |
| Service | none declared |
source trail
Generated from repository data
This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.
Combined YAML source
View the package source record on GitHub.
Used sources
- Geiger risk classifier
- Nucleus package database
- curated configuration and credential file locations
- curated package history
- pkgdb category and tag curation