fastk を Homebrew でインストール

プロジェクトリンク

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コマンドとエイリアス

• FastK
• Fastcat
• Fastcp
• Fastmerge
• Fastmv
• Fastrm
• Haplex
• Histex
• Homex
• KmerMap
• Logex
• Profex
• Symmex
• Tabex
• Vennex

プロジェクトの歴史

The README identifies Gene Myers as author, gives July 22, 2020 as the first date, and documents FastK as a k-mer counter optimized for high-quality assembly datasets. Its command suite includes FastK itself plus utilities for moving, merging, concatenating, inspecting, and mapping FastK output files.

採用の歴史

FastK's public footprint is niche and bioinformatics-specific. Its adoption signal is strongest in packaging and genomics workflows that need efficient k-mer histograms, tables, and profiles for large sequencing data rather than in broad developer communities.

使われ方

FastK consumes CRAM, BAM, SAM, FASTA, FASTQ, gzip-compressed sequence files, and Dazzler databases, producing histograms, sorted k-mer/count tables, and optional sequence profiles. The README emphasizes low-memory operation, temporary disk usage, multithreading, and HPC workflows such as splitting data and merging tables.

パッケージ好きにとっての重要性

For package nerds, FastK is interesting because it is a domain-heavy command suite where filesystem layout is part of the interface: stub files, hidden sidecar files, table/profile extensions, and companion commands such as Fastrm and Fastmerge all have to be packaged together correctly.

タイムライン

• 2020: README records the first FastK date as July 22, 2020.
• 2020: GitHub repository created on October 19, 2020.
• 2021: README current date records April 18, 2021.

Related projects

• KMC3 is named in the README as a performance comparison point.
• DAZZ_DB is supported as an input format.
• merfin is named as a downstream use case for relative k-mer profiles.

ソース

• https://github.com/thegenemyers/FASTK
• https://raw.githubusercontent.com/thegenemyers/FASTK/master/README.md
• https://api.github.com/repos/thegenemyers/FASTK