concoct on Pypi

CONCOCT 1.1.0

A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.

Please Cite

If you use CONCOCT in your publication, please cite:

Johannes Alneberg, Brynjar Smári Bjarnason, Ino de Bruijn, Melanie Schirmer, Joshua Quick, Umer Z Ijaz, Leo Lahti, Nicholas J Loman, Anders F Andersson & Christopher Quince. 2014. Binning metagenomic contigs by coverage and composition. Nature Methods, doi: 10.1038/nmeth.3103

Documentation

A comprehensive documentation for concoct is hosted on readthedocs.

Basic Usage

Cut contigs into smaller parts

cut_up_fasta.py original_contigs.fa -c 10000 -o 0 --merge_last -b contigs_10K.bed > contigs_10K.fa

Generate table with coverage depth information per sample and subcontig. This step assumes the directory 'mapping' contains sorted and indexed bam files where each sample has been mapped against the original contigs.

concoct_coverage_table.py contigs_10K.bed mapping/Sample*.sorted.bam > coverage_table.tsv

Run concoct

concoct --composition_file contigs_10K.fa --coverage_file coverage_table.tsv -b concoct_output/

Merge subcontig clustering into original contig clustering

merge_cutup_clustering.py concoct_output/clustering_gt1000.csv > concoct_output/clustering_merged.csv

Extract bins as individual FASTA

mkdir concoct_output/fasta_bins
extract_fasta_bins.py original_contigs.fa concoct_output/clustering_merged.csv --output_path concoct_output/fasta_bins