Description

MaxBin is a software that is capable of clustering metagenomic contigs

Input

Name (Type)
Description
Pattern

meta (map)

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

]

contigs (file)

Multi FASTA file containing assembled contigs of a given sample

*.fasta

reads (file)

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

*.fasta

abund (file)

Contig abundance files, i.e. reads against each contig. See MaxBin2 README for details. Do not supply at the same time as read files.

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

binned_fastas (file)

Binned contigs, one per bin designated with numeric IDs

*.fasta.gz

summary (file)

Summary file describing which contigs are being classified into which bin

*.summary

log (file)

Log file recording the core steps of MaxBin algorithm

*.log.gz

marker (file)

Marker gene presence numbers for each bin

*.marker.gz

unbinned_fasta (file)

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

*.noclass.gz

tooshort_fasta (file)

All sequences that do not meet the minimum length threshold.

*.tooshort.gz

marker_genes (file)

All sequences that do not meet the minimum length threshold.

*.marker_of_each_gene.tar.gz
included in
mag
maintainer
Github user jfy133
get in touch
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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