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.