metabat11

Overview

MetaBAT: Metagenome Binning based on Abundance and Tetranucleotide frequency (version 1) by Don Kang ([email protected]), Jeff Froula, Rob Egan, and Zhong Wang ([email protected])

Options

-h [ --help ]

produce help message

-i [ --inFile ] arg

Contigs in (gzipped) fasta file format [Mandatory]

-o [ --outFile ] arg

Base file name 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]

--cvExt

When a coverage file without variance (from third party tools) is used instead of abdFile from jgi_summarize_bam_contig_depths

-p [ --pairFile ] 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]

--p1 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)

--p2 arg (=0)

Probability cutoff for secondary neighbors. It supports p1 and better be close to p1. (Percentage; Should be between 0 and 100)

--minProb arg (=0)

Minimum probability for binning consideration. It controls sensitivity. Usually it should be >= 75. (Percentage; Should be between 0 and 100)

--minBinned 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)

--verysensitive

For greater sensitivity, especially in a simple community. It is the shortcut for --p1 90 --p2 85 --pB 20 --minProb 75 --minBinned 20 --minCorr 90

--sensitive

For better sensitivity [default]. It is the shortcut for --p1 90 --p2 90 --pB 20 --minProb 80 --minBinned 40 --minCorr 92

--specific

For better specificity. Different from --sensitive when using correlation binning or ensemble binning. It is the shortcut for --p1 90 --p2 90 --pB 30 --minProb 80 --minBinned 40 --minCorr 96

--veryspecific

For greater specificity. No correlation binning for short contig recruiting. It is the shortcut for --p1 90 --p2 90 --pB 40 --minProb 80 --minBinned 40

--superspecific

For the best specificity. It is the shortcut for --p1 95 --p2 90 --pB 50 --minProb 80 --minBinned 20

--minCorr 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)

--minSamples arg (=10)

Minimum number of sample sizes for considering correlation based recruiting

-x [ --minCV ] arg (=1)

Minimum mean coverage of a contig to consider for abundance distance calculation in each library

--minCVSum arg (=2)

Minimum total mean coverage of a contig (sum of all libraries) to consider for abundance distance calculation

-s [ --minClsSize ] arg (=200000) Minimum size of a bin to be considered as the output

-m [ --minContig ] 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.

--minContigByCorr 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)

-t [ --numThreads ] arg (=0)

Number of threads to use (0: use all cores)

--minShared arg (=50)

Percentage cutoff for merging fuzzy contigs

--fuzzy

Binning with fuzziness which assigns multiple memberships of a contig to bins (activated only with --pairFile at the moment)

-l [ --onlyLabel ]

Output only sequence labels as a list in a column without sequences

-S [ --sumLowCV ]

If set, then every sample that falls below the minCV will be used in an aggregate sample

-V [ --maxVarRatio ] arg (=0)

Ignore any contigs where variance / mean exceeds this ratio (0 disables)

--saveTNF arg

File to save (or load if exists) TNF matrix for each contig in input

--saveDistance arg

File to save (or load if exists) distance graph at lowest probability cutoff

--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

-B [ --B ] arg (=20)

Number of bootstrapping for ensemble binning (Recommended to be >=20)

--pB arg (=50)

Proportion of shared membership in bootstrapping. Major control for sensitivity/specificity. The higher, the specific. (Percentage; Should be between 0 and 100)

--seed arg (=0)

For reproducibility in ensemble binning, though it might produce slightly different results. (0: use random seed)

--keep

Keep the intermediate files for later usage

-d [ --debug ]

Debug output

-v [ --verbose ]

Verbose output