metabat21

Overview

MetaBAT: Metagenome Binning based on Abundance and Tetranucleotide frequency (version 2) by Don Kang ([email protected]), Feng Li, Jeff Froula, Rob Egan, and Zhong Wang ([email protected])

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