TRIM_PIPELINE(1)

📦 version 1.3.10, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 TRIM_PIPELINE(1) 💖

okay so bestie, this is the manual page for trim_pipeline, living in the User Commands section of the manual. She's a whole queen, let's get into it 🫶

✨ NAME ✨

trim_pipeline — the trim pipeline of the PALEOMIX suite, no cap 💅

🌸 SYNOPSIS 🌸

trim_pipeline [options]

🦋 DESCRIPTION 🦋

The PALEOMIX pipelines are literally a set of pipelines and tools designed to aid the rapid processing of High-Throughput Sequencing (HTS) data, and the way that they just do that? Iconic. Here's the lineup, bestie:

  • The BAM pipeline processes de-multiplexed reads from one or more samples, through sequence processing and alignment, to generate BAM alignment files useful in downstream analyses 🧬
  • the Phylogenetic pipeline carries out genotyping and phylogenetic inference on BAM alignment files, either produced using the BAM pipeline or generated elsewhere 🌳
  • and the Zonkey pipeline carries out a suite of analyses on low coverage equine alignments, in order to detect the presence of F1-hybrids in archaeological assemblages 🐴

In addition, PALEOMIX aids in metagenomic analysis of the extracts. Obsessed honestly.

The pipelines have been designed with ancient DNA (aDNA) in mind, and includes several features especially useful for the analyses of ancient samples, but can all be for the processing of modern samples, in order to ensure consistent data processing ✨

trim_pipeline is the trim pipeline of paleomix(1). She's the moment, fr fr 👑

🎀 OPTIONS 🎀

  • trim_pipeline help — Display this message 💬
  • trim_pipeline example [...] — Create example project in folder 📁
  • trim_pipeline makefile [...] — Print makefile template 📝
  • trim_pipeline dryrun [...] — Perform dry run of pipeline on provided makefiles. Equivalent to 'bam_pipeline run --dry-run [...]' 🏃♀️
  • trim_pipeline run [...] — Run pipeline on provided makefiles 🔥
  • trim_pipeline remap [...] — Re-map hits from previous alignment 🔁

💜 SEE ALSO 💜

paleomix(1)

🌈 AUTHOR 🌈

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program 🫶

and that's the whole vibe check, bestie — trim_pipeline 1.2.7, dating all the way back to February 2017, still serving looks in the TRIM_PIPELINE(1) section of your manual. periodt 💅✨🎀

📦 where this page comes from