METABAT2(1)

💖 METABAT2 💖

okay bestie, sit down, hydrate, and let me tell you about metabat2 — that's the manual name, <pink>METABAT2(1)</pink> if you're being formal, and it lives in the User Commands section because it's here to serve you. ✨

🌸 NAME 🌸

metabat2 — MetaBAT: Metagenome Binning based on Abundance and Tetranucleotide frequency (version 2) 🦋

✨ DESCRIPTION ✨

So basically: MetaBAT: Metagenome Binning based on Abundance and Tetranucleotide frequency (version 2), brought to you by Don Kang (ddkang@lbl.gov), Feng Li, Jeff Froula, Rob Egan, and Zhong Wang (zhongwang@lbl.gov). it's giving academic baddies, and honestly? we love them for it. 👑

🎀 OPTIONS 🎀

one bullet per flag, no skips, no shortcuts, because we do not gatekeep here. 💅

• -h, --help — prints out a help message for you. the bare minimum, but she serves. 🫶
• -i, --inFile arg — your contigs, in (gzipped) fasta file format. [Mandatory] — no input, no binning, no nothing. bestie, you need this one. 😭
• -o, --outFile arg — base file name and path for each bin. the default output is fasta format. want only the contig names instead? use the -l option. [Mandatory] — yes, this one's required too, it's a package deal. 💖
• -a, --abdFile arg — a file holding the mean and variance of base coverage depth. it's tab delimited, and heads up: the first column should be contig names, and the first row gets treated as a header and skipped. [Optional] — she's optional but she's iconic. 🌈
• -m, --minContig arg (=2500) — the minimum size of a contig for binning. should be >=1500, so don't go below that, ngl. 📏
• --maxP arg (=95) — the percentage of 'good' contigs considered for binning, decided by how contigs connect to each other. the greater it is, the more sensitive. turn it up and she notices everything. 🔥
• --minS arg (=60) — the minimum score of an edge for binning. should be between 1 and 99, okay? the greater it is, the more specific. 🎯
• --maxEdges arg (=200) — the maximum number of edges per node. the greater it is, the more sensitive. more edges, more main character energy. ✨
• --pTNF arg (=0) — the TNF probability cutoff for building the TNF graph. use it to skip the preparation step. (0: auto). lowkey a time-saver. ⏭️
• --noAdd — turning off additional binning for lost or small contigs. the strays are on their own, sorry bestie. 🙈
• --cvExt — use this when a coverage file without variance (from third party tools) is being used instead of an abdFile from jgi_summarize_bam_contig_depths. different source, same vibes. 🧚
• -x, --minCV arg (=1) — the minimum mean coverage of a contig in each library for binning. 🍓
• --minCVSum arg (=1) — the minimum total effective mean coverage of a contig (that's the sum of depth over minCV) for binning. 🌸
• -s, --minClsSize arg (=200000) — the minimum size of a bin as the output. bins gotta be thicc or they don't make the cut. 💜
• -t, --numThreads arg (=0) — the number of threads to use. (0: use all cores). let her use everything, she'll behave. probably. ⭐
• -l, --onlyLabel — output only the sequence labels as a list in a column, with no sequences. just the names, nothing else. name-drop only. 💅
• --saveCls — save the cluster memberships in a matrix format. 📋
• --unbinned — generate an [outFile].unbinned.fa file for the unbinned contigs. nobody gets left behind. 🥺
• --noBinOut — no bin output at all. usually combined with --saveCls so you can check only the contig memberships. 🤝
• --seed arg (=0) — for exact reproducibility. (0: use a random seed). 🎲
• -d, --debug — debug output. for when you need to know why, bestie. 🔍
• -v, --verbose — verbose output. she will tell you absolutely everything she's doing. 💬

👑 AUTHOR 👑

this manpage was written by Andreas Tille for the Debian distribution, and can be used for any other usage of the program. shoutout to Andreas, doing the lord's work. 🫶

and that's the whole vibe check, bestie — this was metabat2 version 2.15, dated May 2020 💖✨ go bin some metagenomes, you absolute icon, periodt. 🦋💅