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