PALEOMIX(1)

💖 PALEOMIX(1) — the manual page, but make it a vibe 💖

okay bestie, pull up a chair, we're reading paleomix(1) together and honestly? it's a whole personality.

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✨ NAME ✨

paleomix — pipelines and tools for HTS data analyses 🧬🌸

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✨ SYNOPSIS ✨

paleomix <command> [options]

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✨ DESCRIPTION ✨

So the PALEOMIX pipelines are, like, a whole set of pipelines and tools built to help you rapidly process High-Throughput Sequencing (HTS) data. Rapidly. Bestie, we are not waiting around. 🏃‍♀️💨

Let me break down the squad:

• The BAM pipeline takes de-multiplexed reads from one or more samples, runs them through sequence processing and alignment, and spits out BAM alignment files that are actually useful for downstream analyses. It's giving glow-up, honestly.
• The Phylogenetic pipeline does genotyping and phylogenetic inference on BAM alignment files — whether those came from the BAM pipeline or were generated elsewhere (no judgement, we love an outside file 💅).
• The Zonkey pipeline runs a whole suite of analyses on low coverage equine alignments, all so it can detect whether there are F1-hybrids hanging out in archaeological assemblages. Zonkey. I know. Iconic name. 🦓
• And on top of all that, PALEOMIX also helps with metagenomic analysis of the extracts. Versatile queen. 👑

Here's the thing though — the pipelines were designed with ancient DNA (aDNA) in mind, so they include several features that are especially useful for analysing ancient samples. But (and this is important) they can all be used for processing modern samples too, so that your data processing stays consistent across the board. Equality. Consistency. Slay. ✨

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✨ OPTIONS ✨

🌸 Pipelines

• paleomix bam_pipeline — the pipeline for trimming and mapping of NGS reads. The main character, fr fr.
• paleomix trim_pipeline — literally equivalent to 'bam_pipeline', except it only runs the trimming steps. Trimming-only era. ✂️
• paleomix phylo_pipeline — the pipeline for genotyping and phylogenetic inference from BAMs. 🌳
• paleomix zonkey — the pipeline for detecting F1 (equine) hybrids. 🦄

🌸 BAM/SAM tools:

• paleomix cleanup — reads a SAM file from STDIN, and outputs a sorted, tagged, and filter BAM, for which the NM and MD tags have been updated. (Yes, the original says "filter BAM". We're keeping it exactly as written, no cap.) 🧼
• paleomix coverage — calculates coverage across reference sequences or regions of interest. 📏
• paleomix depths — calculates depth histograms across reference sequences or regions of interest. 📊
• paleomix duphist — generates a PCR duplicate histogram; used together with the 'Preseq' tool. 🔁
• paleomix rmdup_collapsed — filters PCR duplicates for collapsed pairedended reads generated by the AdapterRemoval tool. (Pairedended. That's the spelling in the original. We do not touch it. 🫶)

🌸 VCF/GTF/BED/Pileup tools:

• paleomix genotype — creates a bgzipped VCF for a set of (sparse) BED regions, or for entire chromosomes / contigs, using SAMTools / BCFTools. 🧬
• paleomix gtf_to_bed — converts a GTF file into BED files grouped by feature (coding, RNA, etc). 🔄
• paleomix sample_pileup — randomly samples sites in a pileup to generate a FASTA sequence. 🎲
• paleomix vcf_filter — quality filters for VCF records, similar to 'vcfutils.pl varFilter'. 🧹
• paleomix vcf_to_fasta — creates the most likely FASTA sequence from a tabixindexed VCF file. ⭐

🌸 Misc tools:

• paleomix cat — a generalized cat command for gz, bz2 and uncompressed files. 🐱

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✨ AUTHOR ✨

Bestie, if you make use of PALEOMIX in your work, please cite it. This is not optional energy, this is "credit the devs" energy. 🙏

The citation, verbatim, because we respect the science:

Schubert et al, "Characterization of ancient and modern genomes
by SNP detection and phylogenomic and metagenomic analysis using
PALEOMIX".  Nature Protocols. 2014 May; 9(5): 1056-82. doi:
10.1038/nprot.2014.063

And this manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program. 💜

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and that's the whole page, bestie — paleomix version 1.2.7, dated February 2017. go forth and process your HTS data, you absolute icon. periodt. 💅✨🎀