Fast SRA downloader and FASTQ converter, written in pure Rust.
- Fast -- 5-12x 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 | 0.15 s | 1.78 s | 1.94 s | 12.3x |
| SRR2584863 | 288 MiB | 1.07 s | 5.53 s | 12.99 s | 5.2x |
| ERR1018173 | 1.94 GiB | 6.45 s | 33.41 s | -- | 5.2x |
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 |
145.1 ± 2.3 | 141.7 | 149.8 | 1.00 |
fasterq-dump |
1782.6 ± 11.7 | 1769.3 | 1794.4 | 12.28 ± 0.21 |
fastq-dump |
1942.0 ± 3.6 | 1938.0 | 1945.6 | 13.38 ± 0.22 |
SRR2584863 (288 MiB, Illumina paired)
| Command | Mean [s] | Min [s] | Max [s] | Relative |
|---|---|---|---|---|
sracha |
1.070 ± 0.006 | 1.064 | 1.076 | 1.00 |
fasterq-dump |
5.526 ± 0.081 | 5.441 | 5.602 | 5.16 ± 0.08 |
fastq-dump |
12.989 ± 0.031 | 12.967 | 13.025 | 12.14 ± 0.07 |
ERR1018173 (1.94 GiB, 15.6M spots, Illumina paired, single run)
| Command | Time [s] |
|---|---|
sracha |
6.45 |
fasterq-dump |
33.41 |
sracha gzip overhead (SRR28588231, default --gzip-level 1)
| Command | Mean [ms] | Min [ms] | Max [ms] | Relative |
|---|---|---|---|---|
sracha (no compression) |
150.4 ± 2.5 | 145.7 | 154.4 | 1.00 |
sracha (gzip) |
213.7 ± 2.8 | 208.9 | 218.3 | 1.42 ± 0.03 |
Benchmarks run with sracha v0.3.8, 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.
In Nextflow, point a process at the image directly
or let the conda directive resolve it:
process SRACHA_GET {
container 'quay.io/biocontainers/sracha:0.3.7--h54198d6_0'
// or: conda 'bioconda::sracha=0.3.7'
// ...
}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