Fast SRA downloader and FASTQ converter, written in pure Rust.
- Fast -- 5-13x faster than
fasterq-dumpon typical SRA files - One command -- download, convert to FASTQ, and compress
- Batch input -- accessions, BioProjects (PRJNA), studies (SRP), or a file via
--accession-list - gzip or zstd output -- parallel compression, or plain FASTQ
- FASTA output --
--fastadrops quality scores - SRA and SRA-lite -- full or simplified quality scores
- Split modes -- split-3, split-files, split-spot, interleaved
- Resumable downloads -- picks up where it left off
- Stdout streaming --
-Zpipes FASTQ straight into downstream tools - Integrity checks -- MD5 verification on download and decode, plus strict
checks that refuse to write records sracha cannot vouch for (
--no-strictdowngrades them to warnings;--verifyadditionally checks quality values against the archive's recorded histogram) - Platform support -- Illumina, BGISEQ/DNBSEQ, Element, Ultima, PacBio, Nanopore (legacy 454, SOLiD, Ion Torrent, Helicos and Capillary are declined with a clear error)
- Single static binary -- no Python, no C dependencies
# Download, convert, and compress
sracha get SRR28588231
# Download all runs from a BioProject
sracha get PRJNA675068
# Batch download from an accession list
sracha get --accession-list SRR_Acc_List.txt
# Just download
sracha fetch SRR28588231
# Convert a local .sra file
sracha fastq SRR28588231.sra
# Show accession info
sracha info SRR28588231
# Validate a downloaded file
sracha validate SRR28588231.sraUncompressed output, measured with hyperfine.
| File | Size | sracha | fasterq-dump | fastq-dump | Speedup vs fasterq-dump |
|---|---|---|---|---|---|
| SRR28588231 | 23 MiB | 0.14 s | 1.81 s | 1.95 s | 13.1x |
| SRR2584863 | 288 MiB | 1.02 s | 5.63 s | 12.99 s | 5.5x |
| ERR1018173 | 1.94 GiB | 6.26 s | 33.96 s | -- | 5.4x |
sracha produces gzipped FASTQ by default (level 1, ~1.4× the
uncompressed time on small files thanks to parallel block compression),
so the integrated pipeline (sracha get) writes ready-to-use .fastq.gz
without a separate gzip step.
Full hyperfine output
SRR28588231 (23 MiB, 66K spots, Illumina paired)
| Command | Mean [ms] | Min [ms] | Max [ms] | Relative |
|---|---|---|---|---|
sracha |
138.2 ± 2.5 | 134.8 | 145.0 | 1.00 |
fasterq-dump |
1812.0 ± 21.6 | 1791.4 | 1844.1 | 13.11 ± 0.28 |
fastq-dump |
1951.8 ± 5.6 | 1944.4 | 1956.7 | 14.13 ± 0.26 |
SRR2584863 (288 MiB, Illumina paired)
| Command | Mean [s] | Min [s] | Max [s] | Relative |
|---|---|---|---|---|
sracha |
1.021 ± 0.010 | 1.011 | 1.031 | 1.00 |
fasterq-dump |
5.633 ± 0.177 | 5.441 | 5.790 | 5.52 ± 0.18 |
fastq-dump |
12.986 ± 0.019 | 12.973 | 13.008 | 12.71 ± 0.13 |
ERR1018173 (1.94 GiB, 15.6M spots, Illumina paired, single run)
| Command | Time [s] |
|---|---|
sracha |
6.26 |
fasterq-dump |
33.96 |
sracha gzip overhead (SRR28588231, default --gzip-level 1)
| Command | Mean [ms] | Min [ms] | Max [ms] | Relative |
|---|---|---|---|---|
sracha (no compression) |
138.1 ± 2.7 | 133.7 | 143.5 | 1.00 |
sracha (gzip) |
204.6 ± 1.7 | 202.3 | 208.8 | 1.48 ± 0.03 |
Benchmarks run with sracha v0.3.10, sra-tools v3.4.1, on Linux
(8 CPUs). Install the reference toolkit with pixi run install-sratools
and reproduce with validation/benchmark.sh.
Install via Bioconda:
pixi add bioconda::srachaOr download pre-built binaries from the releases page, or install from source:
cargo install --git https://github.com/rnabioco/sracha-rs srachaThe release page covers Linux (x86_64, aarch64), macOS (Intel, Apple
silicon), and Windows (x86_64) — a .tar.gz per Unix target and a .zip for
Windows.
On Linux and macOS x86_64 there are two variants per platform: pick -v2
(the safe default — runs on any CPU since ~2009), or -v3 for extra SIMD
throughput on Haswell-or-newer (2013+) hardware. A -v3 binary aborts with an
illegal-instruction fault at startup on older CPUs, so prefer -v2 unless you
know the host has AVX2. ARM (aarch64) and Windows builds ship a single
binary.
Windows users: take the .zip from the release page, or build with
cargo install above. Bioconda cannot help here — it builds for Linux and
macOS only, and never for Windows, so bioconda::sracha and the
BioContainers images below are unavailable on Windows. (Running sracha under
WSL2 also works, and gets you the Bioconda package.)
To build from source tuned for the current machine, set
RUSTFLAGS="-C target-cpu=native" before cargo install/cargo build --release.
Because sracha is on Bioconda, BioContainers automatically publishes a Docker/Singularity image for every release — no local build required.
# Docker / Podman
docker run --rm quay.io/biocontainers/sracha:0.7.0--h54198d6_0 sracha --help
# Singularity / Apptainer
singularity run \
https://depot.galaxyproject.org/singularity/sracha:0.7.0--h54198d6_0 sracha --helpThese tags track the current Bioconda release and are refreshed weekly by a
CI job. BioContainers builds an image a day or two behind a new release, so
just after a release the tag here may still name the previous version — see
quay.io for every
published <version>--<build> tag.
Using sracha in a workflow manager? See Nextflow and workflow integration in the docs.
Full CLI reference and usage guide: https://rnabioco.github.io/sracha-rs/
sracha builds on the Sequence Read Archive, maintained by the National Center for Biotechnology Information at the National Library of Medicine. The SRA and its toolchain are public-domain software developed by U.S. government employees — our tax dollars at work. Special thanks to Kenneth Durbrow (@durbrow) and the SRA Toolkit team for building and maintaining the infrastructure that makes projects like this possible.
This project wouldn't exist without NCBI's open infrastructure: the VDB/KAR format, the SDL locate API, EUtils, and public S3 hosting of sequencing data. sracha aims to make it easier for the community to build on that foundation.
MIT