CONCOCT Scripts

CONCOCT ships with some additional scripts which are very useful to e.g. create input files and to extract output fastas for concoct. These scripts are:

• cut_up_fasta.py
• concoct_coverage_table.py
• merge_cutup_clustering.py
• extract_fasta_bins.py

The repository CONCOCT contains additional scripts in the CONCOCT/scripts directory which are not fully maintained. They implement methods that we apply after binning with CONCOCT and it might be useful as a starting point or inspiration when creating your own scripts for downstream processing of the output files. Out of these scripts, the ones documented here are:

• dnadiff_dist_matrix.py
• extract_scg_bins.py [Deprecated]

Contents:

• cut_up_fasta.py
  • Usage
  • Example
• concoct_coverage_table.py
  • Usage
  • Example
• merge_cutup_clustering.py
  • Usage
  • Example
• extract_fasta_bins.py
  • Usage
  • Example
• dnadiff_dist_matrix.py
  • Usage
  • Example
• [Deprecated] extract_scg_bins.py
  • Usage
  • Example