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
- Platform support -- Illumina, BGISEQ/DNBSEQ, Element, Ultima, PacBio, Nanopore (legacy 454 and Ion Torrent are not supported)
- 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 srachaOn x86_64 the release page carries 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 builds (aarch64) ship a single binary.
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:0.3.7--h54198d6_0 sracha --help
# Singularity / Apptainer
singularity run \
https://depot.galaxyproject.org/singularity/sracha:0.3.7--h54198d6_0 sracha --helpThe tags above are examples — check
quay.io for the
latest <version>--<build> tag and substitute it in.
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