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Badge](https://anaconda.org/bioconda/sracha/badges/downloads.svg?v=3)](https://anaconda.org/bioconda/sracha)\n\nFast SRA downloader and FASTQ converter, written in pure Rust.\n\n![sracha demo](docs/images/readme.gif)\n\n## Features\n\n- **Fast** -- 4-11x faster than `fasterq-dump` on typical SRA files\n- **One command** -- download, convert to FASTQ, and compress\n- **Batch input** -- accessions, BioProjects (PRJNA), studies (SRP), or a file via `--accession-list`\n- **gzip or zstd output** -- parallel compression, or plain FASTQ\n- **FASTA output** -- `--fasta` drops quality scores\n- **SRA and SRA-lite** -- full or simplified quality scores\n- **Split modes** -- split-3, split-files, split-spot, interleaved\n- **Resumable downloads** -- picks up where it left off\n- **Stdout streaming** -- `-Z` pipes FASTQ straight into downstream tools\n- **Integrity checks** -- MD5 verification on download and decode\n- **Platform support** -- Illumina, BGISEQ/DNBSEQ, Element, Ultima, PacBio, Nanopore (legacy 454 and Ion Torrent are not supported)\n- **Single static binary** -- no Python, no C dependencies\n\n## Quick start\n\n```bash\n# Download, convert, and compress\nsracha get SRR28588231\n\n# Download all runs from a BioProject\nsracha get PRJNA675068\n\n# Batch download from an accession list\nsracha get --accession-list SRR_Acc_List.txt\n\n# Just download\nsracha fetch SRR28588231\n\n# Convert a local .sra file\nsracha fastq SRR28588231.sra\n\n# Show accession info\nsracha info SRR28588231\n\n# Validate a downloaded file\nsracha validate SRR28588231.sra\n```\n\n## Benchmarks\n\n### Local decode (SRA file on disk → FASTQ)\n\nUncompressed output, measured with\n[hyperfine](https://github.com/sharkdp/hyperfine).\n\n| File | Size | sracha | fasterq-dump | fastq-dump | Speedup vs fasterq-dump |\n|:---|---:|---:|---:|---:|---:|\n| SRR28588231 | 23 MiB | 0.17 s | 1.86 s | 2.09 s | **10.9x** |\n| SRR2584863 | 288 MiB | 1.51 s | 5.80 s | 13.30 s | **3.8x** |\n| ERR1018173 | 1.94 GiB | 9.40 s | 34.35 s | -- | **3.7x** |\n\n`sracha` produces gzipped FASTQ by default (level 1, ~1.4× the\nuncompressed time on small files thanks to parallel block compression),\nso the integrated pipeline (`sracha get`) writes ready-to-use `.fastq.gz`\nwithout a separate gzip step.\n\n\u003cdetails\u003e\n\u003csummary\u003eFull hyperfine output\u003c/summary\u003e\n\n**SRR28588231 (23 MiB, 66K spots, Illumina paired)**\n\n| Command | Mean [ms] | Min [ms] | Max [ms] | Relative |\n|:---|---:|---:|---:|---:|\n| `sracha` | 170.9 ± 1.8 | 168.2 | 175.4 | 1.00 |\n| `fasterq-dump` | 1856.4 ± 14.2 | 1838.3 | 1871.6 | 10.86 ± 0.14 |\n| `fastq-dump` | 2090.5 ± 33.3 | 2052.5 | 2125.0 | 12.23 ± 0.23 |\n\n**SRR2584863 (288 MiB, Illumina paired)**\n\n| Command | Mean [s] | Min [s] | Max [s] | Relative |\n|:---|---:|---:|---:|---:|\n| `sracha` | 1.512 ± 0.018 | 1.496 | 1.532 | 1.00 |\n| `fasterq-dump` | 5.799 ± 0.130 | 5.667 | 5.927 | 3.83 ± 0.10 |\n| `fastq-dump` | 13.297 ± 0.157 | 13.192 | 13.478 | 8.79 ± 0.15 |\n\n**ERR1018173 (1.94 GiB, 15.6M spots, Illumina paired, single run)**\n\n| Command | Time [s] |\n|:---|---:|\n| `sracha` | 9.40 |\n| `fasterq-dump` | 34.35 |\n\n**sracha gzip overhead (SRR28588231, default `--gzip-level 1`)**\n\n| Command | Mean [ms] | Min [ms] | Max [ms] | Relative |\n|:---|---:|---:|---:|---:|\n| `sracha (no compression)` | 172.1 ± 5.6 | 165.1 | 185.6 | 1.00 |\n| `sracha (gzip)` | 239.5 ± 5.9 | 230.9 | 249.4 | 1.39 ± 0.06 |\n\n\u003c/details\u003e\n\nBenchmarks run with `sracha` v0.3.5, `sra-tools` v3.4.1, on Linux\n(8 CPUs). Install the reference toolkit with `pixi run install-sratools`\nand reproduce with `validation/benchmark.sh`.\n\n## Installation\n\nInstall via [Bioconda](https://bioconda.github.io/):\n\n```bash\npixi add --channel bioconda sracha\n```\n\nOr download pre-built binaries from the\n[releases page](https://github.com/rnabioco/sracha-rs/releases),\nor install from source:\n\n```bash\ncargo install --git https://github.com/rnabioco/sracha-rs sracha\n```\n\n## Documentation\n\nFull CLI reference and usage guide: \u003chttps://rnabioco.github.io/sracha-rs/\u003e\n\n## Acknowledgments\n\nsracha builds on the [Sequence Read Archive](https://www.ncbi.nlm.nih.gov/sra),\nmaintained by the [National Center for Biotechnology Information](https://www.ncbi.nlm.nih.gov/)\nat the National Library of Medicine. The SRA and its\n[toolchain](https://github.com/ncbi/sra-tools) are public-domain software\ndeveloped by U.S. government employees — our tax dollars at work. Special\nthanks to Kenneth Durbrow ([@durbrow](https://github.com/durbrow)) and the\nSRA Toolkit team for building and maintaining the infrastructure that makes\nprojects like this possible.\n\nThis project wouldn't exist without NCBI's open infrastructure: the\nVDB/KAR format, the SDL locate API, EUtils, and public S3 hosting of\nsequencing data. sracha aims to make it easier for the community to\nbuild on that foundation.\n\n## License\n\nMIT\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frnabioco%2Fsracha-rs","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frnabioco%2Fsracha-rs","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frnabioco%2Fsracha-rs/lists"}