Description

MaxBin is a software that is capable of clustering metagenomic contigs

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

contigs{:bash}

:file

Multi FASTA file containing assembled contigs of a given sample

*.fasta

reads{:bash}

:file

Reads used to assemble contigs in FASTA or FASTQ format. Do not supply at the same time as abundance files.

*.fasta

abund{:bash}

:list

One or more contig abundance files, i.e. average depth of reads against each contig. See MaxBin2 README for details. Do not supply at the same time as read files.

Output

name:type
description
pattern

binned_fastas{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.fasta.gz{:bash}

:file

Binned contigs, one per bin designated with numeric IDs

*.fasta.gz

summary{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.summary{:bash}

:file

Summary file describing which contigs are being classified into which bin

*.summary

abundance{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.abundance{:bash}

:file

Abundance of each bin if multiple abundance files were supplied which bin

*.abundance

log{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.log.gz{:bash}

:file

Log file recording the core steps of MaxBin algorithm

*.log.gz

marker_counts{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.marker.gz{:bash}

:file

Marker counts

*.marker.gz

unbinned_fasta{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.noclass.gz{:bash}

:file

All sequences that pass the minimum length threshold but are not classified successfully.

*.noclass.gz

tooshort_fasta{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.tooshort.gz{:bash}

:file

All sequences that do not meet the minimum length threshold.

*.tooshort.gz

marker_bins{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*_bin.tar.gz{:bash}

:file

Marker bins

*_bin.tar.gz

marker_genes{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*_gene.tar.gz{:bash}

:file

Marker genes

*_gene.tar.gz

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

maxbin2
BSD 3-clause

MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.

sourceforge.net/projects/maxbin 10.1093/bioinformatics/btv638
included in
mag
maintainer
Github user jfy133
get in touch
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