CONCOCT

CONCOCT bins metagenomic contigs into genomes using their sequence composition and their coverage across several samples.

CONCOCT

License

Free to use and open source under the BSD 2-Clause License.

Available

Roihu-CPU: 1.1.0 (module py-concoct), via the bio-apps module.

Usage

CONCOCT is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the CONCOCT module:

module load bio-apps/v202603
module load py-concoct/1.1.0

CONCOCT needs the contigs, and sorted and indexed BAM files from mapping the reads of each sample to the contigs. First cut the contigs into 10 kb pieces and compute the coverage of each piece in each sample:

cut_up_fasta.py contigs.fa -c 10000 -o 0 --merge_last -b contigs_10K.bed > contigs_10K.fa
concoct_coverage_table.py contigs_10K.bed mapping/*.sorted.bam > coverage_table.tsv

Run CONCOCT, with -t giving the number of threads (the default is one thread):

concoct --composition_file contigs_10K.fa --coverage_file coverage_table.tsv \
  -b concoct_output/ -t 16

Merge the clustering of the pieces back to the original contigs, and write each bin to a FASTA file:

merge_cutup_clustering.py concoct_output/clustering_gt1000.csv > concoct_output/clustering_merged.csv
mkdir -p concoct_output/fasta_bins
extract_fasta_bins.py contigs.fa concoct_output/clustering_merged.csv \
  --output_path concoct_output/fasta_bins

To combine the bins of CONCOCT with those of other binning tools, use MAGScoT.

Example batch script

#!/bin/bash
#SBATCH --job-name=concoct
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=12:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=32G

module load bio-apps/v202603
module load py-concoct/1.1.0

cut_up_fasta.py contigs.fa -c 10000 -o 0 --merge_last -b contigs_10K.bed > contigs_10K.fa
concoct_coverage_table.py contigs_10K.bed mapping/*.sorted.bam > coverage_table.tsv
concoct --composition_file contigs_10K.fa --coverage_file coverage_table.tsv \
  -b concoct_output/ -t $SLURM_CPUS_PER_TASK
merge_cutup_clustering.py concoct_output/clustering_gt1000.csv > concoct_output/clustering_merged.csv
mkdir -p concoct_output/fasta_bins
extract_fasta_bins.py contigs.fa concoct_output/clustering_merged.csv \
  --output_path concoct_output/fasta_bins

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk