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Concoct

Concoct stands for Clustering cONtigs with COverage and ComposiTion. This program bins metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Please see the source page, listed below, for more information.

Using the module​

To load Concoct in an interactive session on Palmetto:

module load biocontainers
module load concoct

After loading the biocontainers module, you can see the available commands by running:

report_subtools.sh concoct

Example​

An example analysis command could look as follows:

## Make 10K contigs from full metagenomic contigs file
cut_up_fasta.py <metagenomic_contigs.fasta> -c 10000 -o 0 --merge_last > contigs_10K.fa

## Concoct command
concoct -t $SLURM_CPUS_ON_NODE --composition_file contigs_10K.fa -b <output_folder>

## Merge clustering
merge_cutup_clustering.py <output_folder>/clustering_gt1000.csv > <output_folder>/clustering_merged.csv

## Extract individual FASTA from each bin
mkdir <output_folder>/fasta_bins
extract_fasta_bins.py <metagenomic_contigs.fasta> <output_folder>/clustering_merged.csv --output_path <output_folder>/fasta_bins
tip

concoct and concoct_refine have a multithreading feature! Please try to request additional resources to expedite your analyses! Remember to set the -t flag accordingly!

Please see Concoct source page for more information.

Parallel Capabilities: Single core default, Some tools support Multithreading.