metabat2 - MetaBAT: Metagenome Binning based on Abundance and
Tetranucleotide frequency (version 2)
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)
- -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
This manpage was written by Andreas Tille for the Debian
distribution and
can be used for any other usage of the program.