METABAT1(1)

🌸 metabat1 — like, the manual page, bestie 🌸

okay so real talk: this is the manual page for metabat1, a User Command in section 1 of the manual. Yes, the metabat1. Pull up a chair (or a beanbag, no judgement) because we're doing this together 💖

✨ NAME ✨

metabat1 — MetaBAT: Metagenome Binning based on Abundance and Tetranucleotide frequency (version 1)

💫 DESCRIPTION 💫

MetaBAT: Metagenome Binning based on Abundance and Tetranucleotide frequency (version 1) by Don Kang (ddkang@lbl.gov), Jeff Froula, Rob Egan, and Zhong Wang (zhongwang@lbl.gov).

like. the iconique squad that built the whole thing. we stan 👑

🎀 OPTIONS 🎀

bestie, there are a LOT of these. we're going through every single one, no skipping, no "we'll come back to it later." hydration break whenever you need one 🥤

• -h, --help — produces the help message. the classic "wait what do I do" button. slay.
• -i, --inFile arg — your contigs, in (gzipped) fasta file format. Mandatory, bestie. you literally cannot skip this one, it's giving essential 💅
• -o, --outFile arg — the base file name for each bin. default output is fasta format. wanna output only contig names instead? use the -l option. also Mandatory. no outFile, no vibe.
• -a, --abdFile arg — a file that has the mean and variance of base coverage depth. tab delimited, okay? first column = contig names, and the first row gets treated as a header and skipped. Optional, so breathe. 🫶
• --cvExt — for when you're using a coverage file without variance (from third party tools) instead of the abdFile that comes from jgi_summarize_bam_contig_depths. different source, same dream ✨
• -p, --pairFile arg — a file with paired reads mapping information. use it to boost sensitivity. tab delimited, should have 3 columns: contig index (ordered by), its mate contig index, and supporting mean read coverage. the first row is treated as a header and skipped. Optional 💜
• --p1 arg (=0) — probability cutoff for bin seeding. it's mostly the puppet master of how many potential bins you get and how specific they are. higher value = more (specific) bins. this is a Percentage, should be between 0 and 100.
• --p2 arg (=0) — probability cutoff for secondary neighbors. it's here to support p1, and honestly it should be close to p1. Percentage, between 0 and 100.
• --minProb arg (=0) — minimum probability for binning consideration. this one controls sensitivity. usually it should be >= 75. Percentage, between 0 and 100.
• --minBinned arg (=0) — minimum proportion of already-binned neighbors for one's membership inference. controls specificity. usually it'd be <= 50. Percentage, between 0 and 100.
• --verysensitive — for greater sensitivity, especially in a simple community. it's the shortcut for --p1 90 --p2 85 --pB 20 --minProb 75 --minBinned 20 --minCorr 90.
• --sensitive — for better sensitivity, and it's the default btw. the shortcut for --p1 90 --p2 90 --pB 20 --minProb 80 --minBinned 40 --minCorr 92.
• --specific — for better specificity. it differs from --sensitive when you're using correlation binning or ensemble binning. the shortcut for --p1 90 --p2 90 --pB 30 --minProb 80 --minBinned 40 --minCorr 96.
• --veryspecific — for greater specificity. no correlation binning for short contig recruiting, periodt. the shortcut for --p1 90 --p2 90 --pB 40 --minProb 80 --minBinned 40.
• --superspecific — for the best specificity. the shortcut for --p1 95 --p2 90 --pB 50 --minProb 80 --minBinned 20.
• --minCorr arg (=0) — minimum pearson correlation coefficient for binning missed contigs, to increase sensitivity (super helpful when there are many samples). should be very high (>=90) to reduce contamination. Percentage, between 0 and 100 — and 0 disables it entirely.
• --minSamples arg (=10) — minimum number of sample sizes for considering correlation based recruiting.
• -x, --minCV arg (=1) — minimum mean coverage of a contig to even be considered for abundance distance calculation in each library.
• --minCVSum arg (=2) — minimum total mean coverage of a contig (that's the sum of all libraries) to be considered for abundance distance calculation.
• -s, --minClsSize arg (=200000) — minimum size of a bin to be considered as the output.
• -m, --minContig arg (=2500) — minimum size of a contig to be considered for binning. should be >=1500; ideally >=2500. and listen — if the # of samples is >= minSamples, small contigs (>=1000) get a chance to be recruited to existing bins by default. generous queen 🌸
• --minContigByCorr arg (=1000) — minimum size of a contig to be considered for recruiting by pearson correlation coefficients. activated only if # of samples is >= minSamples, and disabled when minContigByCorr > minContig.
• -t, --numThreads arg (=0) — number of threads to use. 0 means use all cores, go off 🔥
• --minShared arg (=50) — percentage cutoff for merging fuzzy contigs.
• --fuzzy — binning with fuzziness, which assigns multiple memberships of a contig to bins. activated only with --pairFile at the moment, so don't get any ideas 🫣
• -l, --onlyLabel — output only sequence labels as a list in a column, no sequences. just the names, no baggage.
• -S, --sumLowCV — if set, then every sample that falls below the minCV will be used in an aggregate sample. grouping them together, cute.
• -V, --maxVarRatio arg (=0) — ignore any contigs where variance / mean exceeds this ratio. 0 disables it.
• --saveTNF arg — file to save (or load if it exists) the TNF matrix for each contig in the input.
• --saveDistance arg — file to save (or load if it exists) the distance graph at the lowest probability cutoff.
• --saveCls — save cluster memberships as a matrix format.
• --unbinned — generate a [outFile].unbinned.fa file for the unbinned contigs. they're not leftovers, they're independent ✨
• --noBinOut — no bin output. usually paired with --saveCls to check only contig memberships.
• -B, --B arg (=20) — number of bootstrapping for ensemble binning. recommended to be >=20.
• --pB arg (=50) — proportion of shared membership in bootstrapping. the major control for sensitivity/specificity. the higher it is, the more specific. Percentage, between 0 and 100.
• --seed arg (=0) — for reproducibility in ensemble binning, though ngl it might produce slightly different results. 0 means use a random seed 🎲
• --keep — keep the intermediate files for later usage. hoarder-core but valid.
• -d, --debug — debug output.
• -v, --verbose — verbose output. she's chatty and we love her 💬

👑 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 thing, bestie 💖 go bin some metagenomes, you've got this 🦋

signing off from version metabat1 2.15, dated May 2020 — this page has been a whole main character moment and honestly? it ate 💅✨