metabat2 - MetaBAT: Metagenome Binning based on Abundance and Tetranucleotide frequency (version 2)

        This manpage was written by Andreas Tille for the Debian distribution and
        can be used for any other usage of the program.

metabat2 2.15                                       May 2020                                         METABAT2(1)

       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)

       metabat2 - MetaBAT: Metagenome Binning based on Abundance and Tetranucleotide frequency (version 2)

-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