Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
fasta{:bash}
:file
Nucleotide sequences in FASTA format
*.{fasta,fa,fna,faa}
Output
name:type
description
pattern
fasta{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
*.fasta{:bash}
:file
Output fasta file for all the bins reported, optional since it will be created when bins can be found
*.{fasta}
bins{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
*.binning{:bash}
:file
All bins reported
*.{binning}
fm{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
*.fm9{:bash}
:file
FM-index output
*.{fm9}
index{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
*.index{:bash}
:file
1st column contains the original name for each read, 2nd column the index used by CLAME
*.{index}
links{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
*.links{:bash}
:file
Histogram links by number of reads
*.{links}
result{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
*.result{:bash}
:file
Adjacency list for the overlap detected by each read
*.{result}
versions{:bash}
versions.yml{:bash}
: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.
