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seqseeker v0.1.0

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@ethanfenton ethanfenton released this 06 May 18:53
· 6 commits to main since this release
v0.1.0
44fa7e3

Initial release.

What's included

  • C-backed k-mer scanner (~50M reads/min/core), compiles automatically at first use
  • Search for any target sequence via raw string, FASTA file, or built-in name
  • Built-in sequences: eGFP, Venus, mCherry, tdTomato
  • Region selection (full / 5prime / 3prime) to index only part of the target
  • Python package with CLI (seqseeker search/compile/list-sequences) and API
  • R package with Seurat helpers (seqseeker_add_to_seurat)
  • Bash wrapper for cluster environments
  • Zero Python runtime dependencies
  • GitHub Actions CI (Linux + macOS, Python 3.10–3.12)

Install

pip install git+https://github.com/ethanfenton/seqseeker.git
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