{"id":43919144,"url":"https://github.com/vertti/fastqpacker","last_synced_at":"2026-02-06T22:06:44.648Z","repository":{"id":336304320,"uuid":"1149098713","full_name":"vertti/fastqpacker","owner":"vertti","description":"Fast FASTQ compression tool in Go","archived":false,"fork":false,"pushed_at":"2026-02-03T20:01:44.000Z","size":34696,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-02-04T08:35:46.753Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Go","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/vertti.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":"ROADMAP.md","authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2026-02-03T18:08:40.000Z","updated_at":"2026-02-03T20:01:49.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/vertti/fastqpacker","commit_stats":null,"previous_names":["vertti/fastqpacker"],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/vertti/fastqpacker","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vertti%2Ffastqpacker","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vertti%2Ffastqpacker/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vertti%2Ffastqpacker/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vertti%2Ffastqpacker/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/vertti","download_url":"https://codeload.github.com/vertti/fastqpacker/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vertti%2Ffastqpacker/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29178601,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-06T20:14:21.878Z","status":"ssl_error","status_checked_at":"2026-02-06T20:14:21.443Z","response_time":59,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2026-02-06T22:06:39.819Z","updated_at":"2026-02-06T22:06:44.643Z","avatar_url":"https://github.com/vertti.png","language":"Go","funding_links":[],"categories":[],"sub_categories":[],"readme":"# FastQPacker\n\n[![CI](https://github.com/vertti/fastqpacker/actions/workflows/ci.yml/badge.svg)](https://github.com/vertti/fastqpacker/actions/workflows/ci.yml)\n[![Go Report Card](https://goreportcard.com/badge/github.com/vertti/fastqpacker)](https://goreportcard.com/report/github.com/vertti/fastqpacker)\n[![Release](https://img.shields.io/github/v/release/vertti/fastqpacker)](https://github.com/vertti/fastqpacker/releases/latest)\n[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](LICENSE)\n[![Go Reference](https://pkg.go.dev/badge/github.com/vertti/fastqpacker.svg)](https://pkg.go.dev/github.com/vertti/fastqpacker)\n\nThe fastest FASTQ compressor available, with better compression than gzip/pigz/zstd while being 10-80x faster. Specialized tools like DSRC or Spring compress smaller, but are 2-6x slower.\n\nPre-built binaries for macOS and Linux (both ARM and x86_64). Single binary, no dependencies.\n\n## Benchmarks\n\nTested on ERR532393_1 (8.9GB Illumina reads), M4 MacBook Pro:\n\n| Tool | Size | Ratio | Compress | Decompress | Speed |\n|------|------|-------|----------|------------|-------|\n| **fqpack** | **2,826 MB** | **3.2x** | **3.3s** | **3s** | **2,922 MB/s** |\n| DSRC | 2,150 MB | 4.1x | 12s | 18s | 742 MB/s |\n| zstd | 3,312 MB | 2.7x | 11s | 8s | 809 MB/s |\n| pigz | 3,278 MB | 2.7x | 79s | 12s | 113 MB/s |\n| repaq | 5,732 MB | 1.6x | 80s | 27s | 111 MB/s |\n| repaq+xz | 2,761 MB | 3.2x | 388s | 40s | 23 MB/s |\n| 7z | 2,584 MB | 3.4x | 1,442s | 83s | 6 MB/s |\n\nfqpack is **14% smaller than pigz** with **24x faster compression** and **4x faster decompression**. DSRC compresses 24% smaller but is 3.6x slower to compress and 6x slower to decompress. FQSqueezer achieves the best known compression (1,511 MB, 5.9x ratio) but is ~100x slower.\n\n## Installation\n\n```bash\ncurl -fsSL https://raw.githubusercontent.com/vertti/fastqpacker/main/install.sh | sh\n```\n\nOr with Go:\n\n```bash\ngo install github.com/vertti/fastqpacker/cmd/fqpack@latest\n```\n\n## Usage\n\n```bash\n# Compress\nfqpack -i reads.fq -o reads.fqz\n\n# Decompress\nfqpack -d -i reads.fqz -o reads.fq\n\n# Stdin/stdout (Unix pipes)\ncat reads.fq | fqpack -c \u003e reads.fqz\nfqpack -d \u003c reads.fqz \u003e reads.fq\n\n# Control parallelism\nfqpack -w 4 -i reads.fq -o reads.fqz\n```\n\n## How It Works\n\n- **2-bit sequence encoding**: ACGT packed 4 bases per byte (N positions stored separately)\n- **Delta-encoded quality scores**: Adjacent quality scores are similar, deltas compress well\n- **zstd compression**: Modern entropy coding beats gzip's DEFLATE\n- **Parallel block processing**: Scales across all CPU cores\n- **Built-in integrity verification**: CRC32 checksums detect corruption on decompress\n- **Auto-detected quality encoding**: Phred+33 and Phred+64 handled transparently\n\n## Limitations\n\n- Illumina 4-line FASTQ format only (no multi-line sequences)\n- No streaming decompression (full block buffering)\n\n## License\n\nMIT\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvertti%2Ffastqpacker","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvertti%2Ffastqpacker","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvertti%2Ffastqpacker/lists"}