.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH METABAT2 "1" "May 2020" "metabat2 2.15" "User Commands"
.SH NAME
metabat2 \- MetaBAT: Metagenome Binning based on Abundance and Tetranucleotide frequency (version 2)
.SH 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)
.SH OPTIONS
.TP
\fB\-h\fR [ \fB\-\-help\fR ]
produce help message
.TP
\fB\-i\fR [ \fB\-\-inFile\fR ] arg
Contigs in (gzipped) fasta file format [Mandatory]
.TP
\fB\-o\fR [ \fB\-\-outFile\fR ] arg
Base file name and path for each bin. The default output is fasta format.
Use \fB\-l\fR option to output only contig names [Mandatory].
.TP
\fB\-a\fR [ \fB\-\-abdFile\fR ] 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].
.TP
\fB\-m\fR [ \fB\-\-minContig\fR ] arg (=2500)
Minimum size of a contig for binning (should be >=1500).
.TP
\fB\-\-maxP\fR arg (=95)
Percentage of 'good' contigs considered for binning decided by connection
among contigs. The greater, the more sensitive.
.TP
\fB\-\-minS\fR arg (=60)
Minimum score of a edge for binning (should be between 1 and 99). The
greater, the more specific.
.TP
\fB\-\-maxEdges\fR arg (=200)
Maximum number of edges per node. The greater, the more sensitive.
.TP
\fB\-\-pTNF\fR arg (=0)
TNF probability cutoff for building TNF graph. Use it to skip the
preparation step. (0: auto).
.TP
\fB\-\-noAdd\fR
Turning off additional binning for lost or small contigs.
.TP
\fB\-\-cvExt\fR
When a coverage file without variance (from third party tools) is used
instead of abdFile from jgi_summarize_bam_contig_depths.
.TP
\fB\-x\fR [ \fB\-\-minCV\fR ] arg (=1)
Minimum mean coverage of a contig in each library for binning.
.TP
\fB\-\-minCVSum\fR arg (=1)
Minimum total effective mean coverage of a contig (sum of depth over
minCV) for binning.
.HP
\fB\-s\fR [ \fB\-\-minClsSize\fR ] arg (=200000) Minimum size of a bin as the output.
.TP
\fB\-t\fR [ \fB\-\-numThreads\fR ] arg (=0)
Number of threads to use (0: use all cores).
.TP
\fB\-l\fR [ \fB\-\-onlyLabel\fR ]
Output only sequence labels as a list in a column without sequences.
.TP
\fB\-\-saveCls\fR
Save cluster memberships as a matrix format
.TP
\fB\-\-unbinned\fR
Generate [outFile].unbinned.fa file for unbinned contigs
.TP
\fB\-\-noBinOut\fR
No bin output. Usually combined with \fB\-\-saveCls\fR to check only contig
memberships
.TP
\fB\-\-seed\fR arg (=0)
For exact reproducibility. (0: use random seed)
.TP
\fB\-d\fR [ \fB\-\-debug\fR ]
Debug output
.TP
\fB\-v\fR [ \fB\-\-verbose\fR ]
Verbose output
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.