BAM_PIPELINE(1)

💖 BAM_PIPELINE(1) 💖

okay so bestie, welcome to the bam_pipeline manpage, straight outta the User Commands section of your local manual 💅

✨ NAME ✨

bam_pipeline — the BAM pipeline of the PALEOMIX suite, and yes she's iconic for it 🎀

🌸 SYNOPSIS 🌸

bam_pipeline [options]

like. that's it. that's the whole vibe. options go in, magic comes out 🦋

💜 DESCRIPTION 💜

okay so first things first: the PALEOMIX pipelines are a whole set of pipelines and tools built to help you rapidly process High-Throughput Sequencing (HTS) data. rapid processing. we love speed. we love efficiency. main character energy fr fr 🔥

let me break down the trio for you:

• 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 useful for downstream analyses 👑
• the Phylogenetic pipeline does genotyping and phylogenetic inference on BAM alignment files — and those files can come from the BAM pipeline or from literally anywhere else, she's not picky 🧚
• the Zonkey pipeline runs a whole suite of analyses on low coverage equine alignments, all to detect whether there are F1-hybrids hanging out in archaeological assemblages 🐴💀

and that's not even all of it — PALEOMIX also helps out with metagenomic analysis of the extracts. multitasking queen 🌈

these pipelines were designed with ancient DNA (aDNA) in mind, so they pack several features that are especially useful when you're analysing ancient samples. but plot twist: you can use all of them for processing modern samples too, so that your data processing stays consistent across the board. periodt 💅

bam_pipeline is the BAM pipeline of paleomix(1). that's the whole intro, bestie 🫶

⭐ OPTIONS ⭐

here's where it gets juicy. every single one, no skips, no cap:

• bam_pipeline help — displays this message. the classic. the "help me help you" of it all 🙈
• bam_pipeline example [...] — creates an example project in a folder. a little starter kit, a little gift from her to you 🎁
• bam_pipeline makefile [...] — prints out the makefile template. free template, no charge, slay ✨
• bam_pipeline dryrun [...] — performs a dry run of the pipeline on the makefiles you provided. this is equivalent to running bam_pipeline run --dry-run [...] — same thing, different outfit 💅
• bam_pipeline run [...] — runs the pipeline on the makefiles you provided. the real deal, the moment we've all been waiting for 🔥
• bam_pipeline remap [...] — re-maps hits from a previous alignment. round two, but make it alignment 🦋

🦋 SEE ALSO 🦋

• paleomix(1) — go say hi, she's the whole family tree 🌸

🎀 AUTHOR 🎀

this manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program too. generous king, we love to see it 👑

and that's the page, bestie! go process some reads, you absolute legend 💖

and a lil sign-off for the girlies keeping receipts: this is bam_pipeline version 1.2.7, dated February 2017 — the footer said so, and we respect the footer 🎀✨