🌶️ sracha 🌶️

Fast SRA downloader and FASTQ converter, written in pure Rust.

Features

• Parallel downloads -- chunked HTTP Range requests with multiple connections
• Native VDB parsing -- pure Rust, zero C dependencies
• Integrated pipeline -- download, convert, and compress in one command
• Project-level accessions -- pass a BioProject (PRJNA) or study (SRP) to download all runs
• Accession lists -- batch download from a file with --accession-list
• Parallel gzip or zstd -- pigz-style block compression via rayon
• FASTA output -- drop quality scores with --fasta
• SRA and SRA-lite -- full quality or simplified quality scores
• Split modes -- split-3, split-files, split-spot, interleaved
• Platform support -- Illumina, BGISEQ/DNBSEQ, Element, Ultima, PacBio, Nanopore (legacy platforms like 454 and Ion Torrent are not supported)
• Resumable downloads -- picks up where it left off on interruption
• File validation -- verify SRA file integrity

Quick start

# 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.sra

Benchmarks

Local SRA-to-FASTQ conversion (no network), uncompressed output, 8 CPU cores, measured with hyperfine.

File	Size	sracha	fasterq-dump	fastq-dump	Speedup vs fasterq-dump
SRR28588231	23 MiB	0.16 s	1.79 s	1.96 s	11.6x
SRR2584863	288 MiB	1.46 s	5.46 s	13.27 s	3.7x
SRR14724462	3.78 GiB	17.0 s	108.8 s	--	6.4x

Compression adds minimal overhead -- sracha produces gzipped FASTQ by default with parallel block compression, so the integrated pipeline (sracha get) is often faster end-to-end than fasterq-dump followed by a separate gzip step.

Full hyperfine output

SRR28588231 (23 MiB, 66K spots)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
sracha	155.3 ± 1.6	151.8	158.2	1.00
fasterq-dump	1793.9 ± 11.0	1778.1	1806.5	11.55 ± 0.14
fastq-dump	1961.5 ± 2.6	1957.6	1964.5	12.63 ± 0.13

SRR2584863 (288 MiB)

Command	Mean [s]	Min [s]	Max [s]	Relative
sracha	1.456 ± 0.006	1.450	1.461	1.00
fasterq-dump	5.456 ± 0.034	5.429	5.494	3.75 ± 0.03
fastq-dump	13.268 ± 0.049	13.226	13.322	9.11 ± 0.05

SRR14724462 (3.78 GiB, single run)

Command	Time [s]
sracha	17.0
fasterq-dump	108.8

sracha gzip overhead (SRR28588231)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
sracha (no compression)	169.9 ± 51.8	151.9	363.9	1.00
sracha (gzip)	315.2 ± 3.5	310.6	319.4	1.86 ± 0.57

Benchmarks run with sracha v0.1.5, sra-tools v3.2.0, on Linux (8 CPUs). See validation/benchmark.sh to reproduce.

Installation

Install via Bioconda:

pixi add --channel bioconda sracha

Or download pre-built binaries from the releases page, or install from source:

cargo install --git https://github.com/rnabioco/sracha-rs sracha

Documentation

Full CLI reference and usage guide: https://rnabioco.github.io/sracha-rs/

License

MIT