.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH METABAT1 "1" "May 2020" "metabat1 2.15" "User Commands"
.SH NAME
metabat1 \- MetaBAT: Metagenome Binning based on Abundance and Tetranucleotide frequency (version 1)
.SH 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)
.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 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\-\-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\-p\fR [ \fB\-\-pairFile\fR ] 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]
.TP
\fB\-\-p1\fR 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)
.TP
\fB\-\-p2\fR arg (=0)
Probability cutoff for secondary neighbors. It supports p1 and better be
close to p1. (Percentage; Should be between 0 and 100)
.TP
\fB\-\-minProb\fR arg (=0)
Minimum probability for binning consideration. It controls sensitivity.
Usually it should be >= 75. (Percentage; Should be between 0 and 100)
.TP
\fB\-\-minBinned\fR 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)
.TP
\fB\-\-verysensitive\fR
For greater sensitivity, especially in a simple community. It is the
shortcut for \fB\-\-p1\fR 90 \fB\-\-p2\fR 85 \fB\-\-pB\fR 20 \fB\-\-minProb\fR 75 \fB\-\-minBinned\fR 20
\fB\-\-minCorr\fR 90
.TP
\fB\-\-sensitive\fR
For better sensitivity [default]. It is the shortcut for \fB\-\-p1\fR 90 \fB\-\-p2\fR 90
\fB\-\-pB\fR 20 \fB\-\-minProb\fR 80 \fB\-\-minBinned\fR 40 \fB\-\-minCorr\fR 92
.TP
\fB\-\-specific\fR
For better specificity. Different from \fB\-\-sensitive\fR when using correlation
binning or ensemble binning. It is the shortcut for \fB\-\-p1\fR 90 \fB\-\-p2\fR 90 \fB\-\-pB\fR
30 \fB\-\-minProb\fR 80 \fB\-\-minBinned\fR 40 \fB\-\-minCorr\fR 96
.TP
\fB\-\-veryspecific\fR
For greater specificity. No correlation binning for short contig
recruiting. It is the shortcut for \fB\-\-p1\fR 90 \fB\-\-p2\fR 90 \fB\-\-pB\fR 40 \fB\-\-minProb\fR 80
\fB\-\-minBinned\fR 40
.TP
\fB\-\-superspecific\fR
For the best specificity. It is the shortcut for \fB\-\-p1\fR 95 \fB\-\-p2\fR 90 \fB\-\-pB\fR 50
\fB\-\-minProb\fR 80 \fB\-\-minBinned\fR 20
.TP
\fB\-\-minCorr\fR 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)
.TP
\fB\-\-minSamples\fR arg (=10)
Minimum number of sample sizes for considering correlation based
recruiting
.TP
\fB\-x\fR [ \fB\-\-minCV\fR ] arg (=1)
Minimum mean coverage of a contig to consider for abundance distance
calculation in each library
.TP
\fB\-\-minCVSum\fR arg (=2)
Minimum total mean coverage of a contig (sum of all libraries) to
consider for abundance distance calculation
.HP
\fB\-s\fR [ \fB\-\-minClsSize\fR ] arg (=200000) Minimum size of a bin to be considered as the output
.TP
\fB\-m\fR [ \fB\-\-minContig\fR ] 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.
.TP
\fB\-\-minContigByCorr\fR 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)
.TP
\fB\-t\fR [ \fB\-\-numThreads\fR ] arg (=0)
Number of threads to use (0: use all cores)
.TP
\fB\-\-minShared\fR arg (=50)
Percentage cutoff for merging fuzzy contigs
.TP
\fB\-\-fuzzy\fR
Binning with fuzziness which assigns multiple memberships of a contig to
bins (activated only with \fB\-\-pairFile\fR at the moment)
.TP
\fB\-l\fR [ \fB\-\-onlyLabel\fR ]
Output only sequence labels as a list in a column without sequences
.TP
\fB\-S\fR [ \fB\-\-sumLowCV\fR ]
If set, then every sample that falls below the minCV will be used in an
aggregate sample
.TP
\fB\-V\fR [ \fB\-\-maxVarRatio\fR ] arg (=0)
Ignore any contigs where variance / mean exceeds this ratio (0 disables)
.TP
\fB\-\-saveTNF\fR arg
File to save (or load if exists) TNF matrix for each contig in input
.TP
\fB\-\-saveDistance\fR arg
File to save (or load if exists) distance graph at lowest probability
cutoff
.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\-B\fR [ \fB\-\-B\fR ] arg (=20)
Number of bootstrapping for ensemble binning (Recommended to be >=20)
.TP
\fB\-\-pB\fR arg (=50)
Proportion of shared membership in bootstrapping. Major control for
sensitivity/specificity. The higher, the specific. (Percentage; Should be
between 0 and 100)
.TP
\fB\-\-seed\fR arg (=0)
For reproducibility in ensemble binning, though it might produce slightly
different results. (0: use random seed)
.TP
\fB\-\-keep\fR
Keep the intermediate files for later usage
.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.