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CONCOCT Specifications

Process Details

  • Name: CONCOCT
  • Process UUID: f931yt932ata09emb888tr5obcogp0
  • Process Group: Binning

Overview

CONCOCT is a binning tool designed for creating metagenome-assembled genomes (MAGs) from short-read sequencing data. This process clusters contigs into bins based on their composition and coverage patterns, enabling the reconstruction of individual genomes from complex metagenomic assemblies. CONCOCT uses tetranucleotide frequency and differential coverage across samples to group contigs that likely originate from the same organism.

This process is implemented in Bash, which invokes Python scripts from the CONCOCT toolkit for contig fragmentation, coverage calculation, clustering, and bin extraction.

Key Functionality

  • Contig Fragmentation: Cuts assembled contigs into fragments of specified size to improve clustering accuracy
  • Coverage Calculation: Computes coverage depth for each fragment using alignment data from BAM files
  • Composition-based Clustering: Groups fragments based on tetranucleotide frequency patterns and coverage profiles
  • Bin Extraction: Reconstructs complete contigs from clustered fragments and outputs individual FASTA files for each bin

Input/Output Specification

Inputs

Required Inputs

  • Input Directory
    • Description: Directory containing assembled contigs (FASTA format) and sorted alignment files (BAM format with corresponding BAI index)
    • Format: Directory

Outputs

  • Log File

    • Description: Process execution log containing details about input files, clustering statistics, and created bins
    • Format: Log file

  • Output Directory

    • Description: Directory containing binned contigs as separate FASTA files, along with the original assembly file
    • Format: Directory

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Fragment Size

    • Description: Write the desired fragment sizes of bins. The value should be an integer! Don't change unless you know what you're doing!
    • Default value: 10000

  • Minimum Contig Length

    • Description: Write the minimum expected fragment length for Concoct to work on. The value should be an integer!
    • Default value: 2500

  • Overlap Length

    • Description: Write the desired overlap between contigs. The value should be an integer!
    • Default value: 0

References & Resources

  • Tool Documentation: Contact the team for details on cut_up_fasta.py, concoct_coverage_table.py, merge_cutup_clustering.py, and extract_fasta_bins.py
  • Related Papers: Alneberg, J., Bjarnason, B. S., de Bruijn, I., Schirmer, M., Quick, J., Ijaz, U. Z., Lahti, L., Loman, N. J., Andersson, A. F., & Quince, C. (2014). Binning metagenomic contigs by coverage and composition. Nature Methods, 11(11), 1144-1146. https://doi.org/10.1038/nmeth.3103