Description

binning of metagenomic sequences

Input

name:type
description
pattern

meta:map

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

fasta:file

Nucleotide sequences in FASTA format

*.{fasta,fa,fna,faa}

Output

name:type
description
pattern

fasta

meta:map

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

*.fasta:file

Output fasta file for all the bins reported, optional since it will be created when bins can be found

*.{fasta}

bins

meta:map

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

*.binning:file

All bins reported

*.{binning}

fm

meta:map

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

*.fm9:file

FM-index output

*.{fm9}

index

meta:map

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

*.index:file

1st column contains the original name for each read, 2nd column the index used by CLAME

*.{index}

meta:map

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

Histogram links by number of reads

*.{links}

result

meta:map

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

*.result:file

Adjacency list for the overlap detected by each read

*.{result}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

clame
GPLv3

CLAME is a binning software for metagenomic reads. It immplements a fm-index search algorithm for nucleotide sequence alignment. Then it uses strongly connected component strategy to bin sequences with similar DNA composition.