---
name: "metabat2"
section: "1"
platform: "linux"
package: "metabat"
version: "2.15-4+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/metabat2"
---

# metabat2(1)

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

## NAME

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

## DESCRIPTION

MetaBAT: Metagenome Binning based on Abundance and Tetranucleotide frequency (version 2) by Don Kang (ddkang@lbl.gov), Feng Li, Jeff Froula, Rob Egan, and Zhong Wang (zhongwang@lbl.gov)

## OPTIONS

- **-h** \[ **--help** \]

  produce help message

- **-i** \[ **--inFile** \] arg

  Contigs in (gzipped) fasta file format \[Mandatory\]

- **-o** \[ **--outFile** \] arg

  Base file name and path for each bin. The default output is fasta format. Use **-l** option to output only contig names \[Mandatory\].

- **-a** \[ **--abdFile** \] arg

  A file having mean and variance of base coverage depth (tab delimited; the first column should be contig names, and the first row will be considered as the header and be skipped) \[Optional\].

- **-m** \[ **--minContig** \] arg (=2500)

  Minimum size of a contig for binning (should be \>=1500).

- **--maxP** arg (=95)

  Percentage of 'good' contigs considered for binning decided by connection among contigs. The greater, the more sensitive.

- **--minS** arg (=60)

  Minimum score of a edge for binning (should be between 1 and 99). The greater, the more specific.

- **--maxEdges** arg (=200)

  Maximum number of edges per node. The greater, the more sensitive.

- **--pTNF** arg (=0)

  TNF probability cutoff for building TNF graph. Use it to skip the preparation step. (0: auto).

- **--noAdd**

  Turning off additional binning for lost or small contigs.

- **--cvExt**

  When a coverage file without variance (from third party tools) is used instead of abdFile from jgi\_summarize\_bam\_contig\_depths.

- **-x** \[ **--minCV** \] arg (=1)

  Minimum mean coverage of a contig in each library for binning.

- **--minCVSum** arg (=1)

  Minimum total effective mean coverage of a contig (sum of depth over minCV) for binning.

**-s** \[ **--minClsSize** \] arg (=200000) Minimum size of a bin as the output.

- **-t** \[ **--numThreads** \] arg (=0)

  Number of threads to use (0: use all cores).

- **-l** \[ **--onlyLabel** \]

  Output only sequence labels as a list in a column without sequences.

- **--saveCls**

  Save cluster memberships as a matrix format

- **--unbinned**

  Generate \[outFile\].unbinned.fa file for unbinned contigs

- **--noBinOut**

  No bin output. Usually combined with **--saveCls** to check only contig memberships

- **--seed** arg (=0)

  For exact reproducibility. (0: use random seed)

- **-d** \[ **--debug** \]

  Debug output

- **-v** \[ **--verbose** \]

  Verbose output

## AUTHOR

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