Description

Unsupervised binning of metagenomic contigs by using nucleotide composition - kmer frequencies - and coverage data for multiple samples

Input

name:type
description
pattern

meta:map

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

coverage_file:file

Subcontig coverage TSV table (typically generated with concoct_coverage_table.py)

*.tsv

fasta:file

FASTA file containing subcontigs (typically generated with cutup_fasta.py)

*.fasta

Output

name:type
description
pattern

args_txt

meta:map

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

*_args.txt:file

File containing execution parameters

*_args.txt

clustering_csv

meta:map

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

*_clustering_gt1000.csv:file

CSV containing information which subcontig is assigned to which cluster

*_clustering_gt1000.csv

log_txt

meta:map

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

*_log.txt:file

Log file of tool execution

*_log.txt

original_data_csv

meta:map

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

*_original_data_gt1000.csv:file

Original CONCOCT GT1000 output

*_original_data_gt1000.csv

pca_components_csv

meta:map

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

*_PCA_components_data_gt1000.csv:file

Untransformed PCA component values

*_PCA_components_data_gt1000.csv

pca_transformed_csv

meta:map

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

*_PCA_transformed_data_gt1000.csv:file

Transformed PCA component values

*_PCA_transformed_data_gt1000.csv

versions

versions.yml:file

File containing software versions

versions.yml

Tools

concoct
FreeBSD

Clustering cONtigs with COverage and ComposiTion

concoct.readthedocs.io/en/latest https://github.com/BinPro/CONCOCT 10.1038/nmeth.3103
mag
Github user jfy133
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