modules/maxbin2

MaxBin is a software that is capable of clustering metagenomic contigs

metagenomicsassemblybinningmaxbin2de novo assemblymagsmetagenome-assembled genomescontigs

https://github.com/nf-core/modules/[...]/modules/nf-core/maxbin2

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:false ]

`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: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`

`meta:map`

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

`*.fasta.gz:file`

Binned contigs, one per bin designated with numeric IDs

*.fasta.gz

`summary`

`meta:map`

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

`*.summary:file`

Summary file describing which contigs are being classified into which bin

*.summary

`abundance`

`meta:map`

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

`*.abundance:file`

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

*.abundance

`log`

`meta:map`

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

`*.log.gz:file`

Log file recording the core steps of MaxBin algorithm

*.log.gz

`marker_counts`

`meta:map`

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

`*.marker.gz:file`

Marker counts

*.marker.gz

`unbinned_fasta`

`meta:map`

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

`*.noclass.gz:file`

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

*.noclass.gz

`tooshort_fasta`

`meta:map`

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

`*.tooshort.gz:file`

All sequences that do not meet the minimum length threshold.

*.tooshort.gz

`marker_bins`

`meta:map`

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

`*_bin.tar.gz:file`

Marker bins

*_bin.tar.gz

`marker_genes`

`meta:map`

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

`*_gene.tar.gz:file`

Marker genes

*_gene.tar.gz

`versions`

`versions.yml: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

modules/maxbin2

Description

Input

meta:map

contigs:file

reads:file

abund:list

Output

binned_fastas

meta:map

*.fasta.gz:file

summary

meta:map

*.summary:file

abundance

meta:map

*.abundance:file

log

meta:map

*.log.gz:file

marker_counts

meta:map

*.marker.gz:file

unbinned_fasta

meta:map

*.noclass.gz:file

tooshort_fasta

meta:map

*.tooshort.gz:file

marker_bins

meta:map

*_bin.tar.gz:file

marker_genes

meta:map

*_gene.tar.gz:file

versions

versions.yml:file

Tools

maxbin2 BSD 3-clause

included in

maintainer

get in touch

`meta:map`

`contigs:file`

`reads:file`

`abund:list`

`binned_fastas`

`meta:map`

`*.fasta.gz:file`

`summary`

`meta:map`

`*.summary:file`

`abundance`

`meta:map`

`*.abundance:file`

`log`

`meta:map`

`*.log.gz:file`

`marker_counts`

`meta:map`

`*.marker.gz:file`

`unbinned_fasta`

`meta:map`

`*.noclass.gz:file`

`tooshort_fasta`

`meta:map`

`*.tooshort.gz:file`

`marker_bins`

`meta:map`

`*_bin.tar.gz:file`

`marker_genes`

`meta:map`

`*_gene.tar.gz:file`

`versions`

`versions.yml:file`

maxbin2
BSD 3-clause