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

]

coverage (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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

args_txt (file)

File containing execution parameters

*_args.txt

clustering_csv (file)

CSV containing information which subcontig is assigned to which cluster

*_clustering_gt1000.csv

log_txt (file)

Log file of tool execution

*_log.txt

original_data_csv (file)

Original CONCOCT GT1000 output

*_original_data_gt1000.csv

pca_components_csv (file)

Untransformed PCA component values

*_PCA_components_data_gt1000.csv

pca_transformed_csv (file)

Transformed PCA compontent values

*_PCA_transformed_data_gt1000.csv
included in
mag
author
Github user jfy133
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

concoct
FreeBSD

Clustering cONtigs with COverage and ComposiTion

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