---
name: "metabat1"
section: "1"
platform: "linux"
package: "metabat"
version: "2.15-4+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/metabat1"
---

# metabat1(1)

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

## 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)

## OPTIONS

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

  produce help message

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

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

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

  Base file name 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) \[Optional\]

- **--cvExt**

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

- **-p** \[ **--pairFile** \] arg

  A file having paired reads mapping information. Use it to increase sensitivity. (tab delimited; should have 3 columns of contig index (ordered by), its mate contig index, and supporting mean read coverage. The first row will be considered as the header and be skipped) \[Optional\]

- **--p1** arg (=0)

  Probability cutoff for bin seeding. It mainly controls the number of potential bins and their specificity. The higher, the more (specific) bins would be. (Percentage; Should be between 0 and 100)

- **--p2** arg (=0)

  Probability cutoff for secondary neighbors. It supports p1 and better be close to p1. (Percentage; Should be between 0 and 100)

- **--minProb** arg (=0)

  Minimum probability for binning consideration. It controls sensitivity. Usually it should be \>= 75. (Percentage; Should be between 0 and 100)

- **--minBinned** arg (=0)

  Minimum proportion of already binned neighbors for one's membership inference. It contorls specificity. Usually it would be \<= 50 (Percentage; Should be between 0 and 100)

- **--verysensitive**

  For greater sensitivity, especially in a simple community. It is the shortcut for **--p1** 90 **--p2** 85 **--pB** 20 **--minProb** 75 **--minBinned** 20 **--minCorr** 90

- **--sensitive**

  For better sensitivity \[default\]. It is the shortcut for **--p1** 90 **--p2** 90 **--pB** 20 **--minProb** 80 **--minBinned** 40 **--minCorr** 92

- **--specific**

  For better specificity. Different from **--sensitive** when using correlation binning or ensemble binning. It is 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. It is the shortcut for **--p1** 90 **--p2** 90 **--pB** 40 **--minProb** 80 **--minBinned** 40

- **--superspecific**

  For the best specificity. It is 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 (Helpful when there are many samples). Should be very high (\>=90) to reduce contamination. (Percentage; Should be between 0 and 100; 0 disables)

- **--minSamples** arg (=10)

  Minimum number of sample sizes for considering correlation based recruiting

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

  Minimum mean coverage of a contig to consider for abundance distance calculation in each library

- **--minCVSum** arg (=2)

  Minimum total mean coverage of a contig (sum of all libraries) to consider 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). If # of samples \>= minSamples, small contigs (\>=1000) will be given a chance to be recruited to existing bins by default.

- **--minContigByCorr** arg (=1000)

  Minimum size of a contig to be considered for recruiting by pearson correlation coefficients (activated only if # of samples \>= minSamples; disabled when minContigByCorr \> minContig)

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

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

- **--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)

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

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

- **-S** \[ **--sumLowCV** \]

  If set, then every sample that falls below the minCV will be used in an aggregate sample

- **-V** \[ **--maxVarRatio** \] arg (=0)

  Ignore any contigs where variance / mean exceeds this ratio (0 disables)

- **--saveTNF** arg

  File to save (or load if exists) TNF matrix for each contig in input

- **--saveDistance** arg

  File to save (or load if exists) distance graph at lowest probability cutoff

- **--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

- **-B** \[ **--B** \] arg (=20)

  Number of bootstrapping for ensemble binning (Recommended to be \>=20)

- **--pB** arg (=50)

  Proportion of shared membership in bootstrapping. Major control for sensitivity/specificity. The higher, the specific. (Percentage; Should be between 0 and 100)

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

  For reproducibility in ensemble binning, though it might produce slightly different results. (0: use random seed)

- **--keep**

  Keep the intermediate files for later usage

- **-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.