# Install sratoolkit with Homebrew, Nix Data tools for INSDC Sequence Read Archive. Version 3.4.1 via Homebrew; verified from local package data. Also installable with nix: nix profile install nixpkgs#sratoolkit. ## Install ```sh sudo av install brew:sratoolkit ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install sratoolkit ``` Evidence: local Homebrew formula metadata ### Linux - Nix (92%): ```sh nix profile install nixpkgs#sratoolkit ``` Evidence: nixpkgs package indexes: pkgs/by-name/sr/sratoolkit/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 ## Package facts - **Package key:** brew:sratoolkit - **Package manager:** Homebrew - **Package manager page:** - **Version:** 3.4.1 - **Source summary:** Data tools for INSDC Sequence Read Archive - **Homepage:** - **Repository:** - **License:** LicenseRef-Homebrew-public-domain AND GPL-3.0-or-later AND MIT - **Source archive:** - **Generated:** 2026-08-04T22:13:35+00:00 ## Executables - abi-dump (cli) - abi-dump.3 (cli) - abi-dump.3.4.1 (cli) - align-info (cli) - align-info.3 (cli) - align-info.3.4.1 (cli) - check-corrupt (cli) - check-corrupt.3 (cli) - check-corrupt.3.4.1 (cli) - fasterq-dump (cli) - fasterq-dump-orig.3.4.1 (cli) - fasterq-dump.3 (cli) - fasterq-dump.3.4.1 (cli) - fastq-dump (cli) - fastq-dump-orig.3.4.1 (cli) - fastq-dump.3 (cli) - fastq-dump.3.4.1 (cli) - illumina-dump (cli) - illumina-dump.3 (cli) - illumina-dump.3.4.1 (cli) - kdbmeta (cli) - kdbmeta.3 (cli) - kdbmeta.3.4.1 (cli) - ngs-pileup (cli) - ngs-pileup.3 (cli) - ngs-pileup.3.4.1 (cli) - prefetch (cli) - prefetch-orig.3.4.1 (cli) - prefetch.3 (cli) - prefetch.3.4.1 (cli) - rcexplain (cli) - rcexplain.3 (cli) - rcexplain.3.4.1 (cli) - ref-variation (cli) - ref-variation.3 (cli) - ref-variation.3.4.1 (cli) - sam-dump (cli) - sam-dump-orig.3.4.1 (cli) - sam-dump.3 (cli) - sam-dump.3.4.1 (cli) - sff-dump (cli) - sff-dump.3 (cli) - sff-dump.3.4.1 (cli) - sra-info (cli) - sra-info.3 (cli) - sra-info.3.4.1 (cli) - sra-pileup (cli) - sra-pileup-orig.3.4.1 (cli) - sra-pileup.3 (cli) - sra-pileup.3.4.1 (cli) - sra-search (cli) - sra-search.3 (cli) - sra-search.3.4.1 (cli) - sra-stat (cli) - sra-stat.3 (cli) - sra-stat.3.4.1 (cli) - srapath (cli) - srapath-orig.3.4.1 (cli) - srapath.3 (cli) - srapath.3.4.1 (cli) - sratools (cli) - sratools.3 (cli) - sratools.3.4.1 (cli) - test-sra (cli) - test-sra.3 (cli) - test-sra.3.4.1 (cli) - var-expand (cli) - var-expand.3 (cli) - var-expand.3.4.1 (cli) - vdb-config (cli) - vdb-config.3 (cli) - vdb-config.3.4.1 (cli) - vdb-decrypt (cli) - vdb-decrypt.3 (cli) - vdb-decrypt.3.4.1 (cli) - vdb-dump (cli) - vdb-dump-orig.3.4.1 (cli) - vdb-dump.3 (cli) - vdb-dump.3.4.1 (cli) - vdb-encrypt (cli) - vdb-encrypt.3 (cli) - vdb-encrypt.3.4.1 (cli) - vdb-validate (cli) - vdb-validate.3 (cli) - vdb-validate.3.4.1 (cli) - abi-dump (alias) - abi-dump.3 (alias) - abi-dump.3.4.1 (alias) - align-info (alias) - align-info.3 (alias) - align-info.3.4.1 (alias) - check-corrupt (alias) - check-corrupt.3 (alias) - check-corrupt.3.4.1 (alias) - fasterq-dump (alias) - fasterq-dump-orig.3.4.1 (alias) - fasterq-dump.3 (alias) - fasterq-dump.3.4.1 (alias) - fastq-dump (alias) - fastq-dump-orig.3.4.1 (alias) - fastq-dump.3 (alias) - fastq-dump.3.4.1 (alias) - illumina-dump (alias) - illumina-dump.3 (alias) - illumina-dump.3.4.1 (alias) - kdbmeta (alias) - kdbmeta.3 (alias) - kdbmeta.3.4.1 (alias) - ngs-pileup (alias) - ngs-pileup.3 (alias) - ngs-pileup.3.4.1 (alias) - prefetch (alias) - prefetch-orig.3.4.1 (alias) - prefetch.3 (alias) - prefetch.3.4.1 (alias) - rcexplain (alias) - rcexplain.3 (alias) - rcexplain.3.4.1 (alias) - ref-variation (alias) - ref-variation.3 (alias) - ref-variation.3.4.1 (alias) - sam-dump (alias) - sam-dump-orig.3.4.1 (alias) - sam-dump.3 (alias) - sam-dump.3.4.1 (alias) - sff-dump (alias) - sff-dump.3 (alias) - sff-dump.3.4.1 (alias) - sra-info (alias) - sra-info.3 (alias) - sra-info.3.4.1 (alias) - sra-pileup (alias) - sra-pileup-orig.3.4.1 (alias) - sra-pileup.3 (alias) - sra-pileup.3.4.1 (alias) - sra-search (alias) - sra-search.3 (alias) - sra-search.3.4.1 (alias) - sra-stat (alias) - sra-stat.3 (alias) - sra-stat.3.4.1 (alias) - srapath (alias) - srapath-orig.3.4.1 (alias) - srapath.3 (alias) - srapath.3.4.1 (alias) - sratools (alias) - sratools.3 (alias) - sratools.3.4.1 (alias) - test-sra (alias) - test-sra.3 (alias) - test-sra.3.4.1 (alias) - var-expand (alias) - var-expand.3 (alias) - var-expand.3.4.1 (alias) - vdb-config (alias) - vdb-config.3 (alias) - vdb-config.3.4.1 (alias) - vdb-decrypt (alias) - vdb-decrypt.3 (alias) - vdb-decrypt.3.4.1 (alias) - vdb-dump (alias) - vdb-dump-orig.3.4.1 (alias) - vdb-dump.3 (alias) - vdb-dump.3.4.1 (alias) - vdb-encrypt (alias) - vdb-encrypt.3 (alias) - vdb-encrypt.3.4.1 (alias) - vdb-validate (alias) - vdb-validate.3 (alias) - vdb-validate.3.4.1 (alias) ## Dependencies - hdf5 ## Build dependencies - cmake ## Uses from macOS - libxml2 ## Install behavior - Post-install hook: not defined - Bottle: available on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## Freshness - Page generated: 2026-08-04 - Package-manager version: 3.4.1 - Local data: ok - Upstream repository: https://github.com/ncbi/sra-tools - Upstream latest detected: 3.4.1 (current) - info: No package-manager update timestamp was available. ## 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 - - - - - source_facts.executables - source_facts.package-manager ## Security Notes broad file, network, media, or database tool signal. - **Geiger risk:** blue / medium - broad file, network, media, or database tool signal ## 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 - Unix: ${HOME}/.ncbi/user-settings.mkfg ## Source Database Details - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** sratoolkit - **Version Scheme:** 0 - **Revision:** 0 - **Head Version:** HEAD - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** head, stable ## Other Package-Manager Records - Nix - sratoolkit: normalized package name match | nixpkgs package indexes: pkgs/by-name/sr/sratoolkit/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 ## Related links - [Source-control packages](https://pkg.so/source-control-tools/) - Belongs to a source-control command family. - [Secret-risk packages](https://pkg.so/secret-risk-packages/) - Has protected-tool coverage, approval-gate, or non-low Geiger security signals. - [Terminal utility packages](https://pkg.so/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Archive and compression packages](https://pkg.so/archive-compression-tools/) - Matched archive or compression metadata. - [hdf5](https://pkg.so/brew/hdf5/) - Runtime dependency declared by Homebrew. - [cmake](https://pkg.so/brew/cmake/) - Build dependency declared by Homebrew. - [samtools](https://pkg.so/brew/samtools/) - Shares pkgdb curated category or tags: bioinformatics, cli, science. - [htslib](https://pkg.so/brew/htslib/) - Shares pkgdb curated category or tags: bioinformatics, cli, science. - [blast](https://pkg.so/brew/blast/) - Shares pkgdb curated category or tags: bioinformatics, cli, science. - [bcftools](https://pkg.so/brew/bcftools/) - Shares pkgdb curated category or tags: bioinformatics, cli, science. - [mmseqs2](https://pkg.so/brew/mmseqs2/) - Shares pkgdb curated category or tags: bioinformatics, cli, science. - [seqkit](https://pkg.so/brew/seqkit/) - Shares pkgdb curated category or tags: bioinformatics, cli, science. - [snakemake](https://pkg.so/brew/snakemake/) - Shares pkgdb curated category or tags: bioinformatics, cli, science. - [fastqc](https://pkg.so/brew/fastqc/) - Shares pkgdb curated category or tags: bioinformatics, cli, science. - [chopper](https://pkg.so/brew/chopper/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, data, fastq, read. - [adapterremoval](https://pkg.so/brew/adapterremoval/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, fastq, read, science. - [any2fasta](https://pkg.so/brew/any2fasta/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, conversion, science, sequence. ## Combined YAML source View the package source record on GitHub. [combined/sratoolkit.yml](https://github.com/mxcl/pkgdb/blob/main/combined/sratoolkit.yml) ## Sources - pkg.so package database - Geiger risk classifier - package-page enrichment - curated configuration and credential file locations - curated package history - package version freshness - pkgdb category and tag curation - package relationship graph - external package-manager database matches - cross-ecosystem install command graph