commec: a free, open-source, globally available tool for DNA sequence screening

The commec package is a tool for DNA sequence screening that is part of the Common Mechanism for DNA Synthesis screening. The package offers several sub-commands through the commec entrypoint:

screen  Run Common Mechanism screening on an input FASTA.
flag    Parse .screen.json files in a directory and create a CSV file of outcomes
setup   A command-line helper tool to download the required databases
split   Split a multi-record FASTA file into individual files, one for each record

The commec screen command runs an input FASTA through the following screening steps:

1. Biorisk search: Fast HMM-based search against curated sequence profiles
2. Taxonomy Search: look for best matches to regulated pathogens using a two-step process:
   • Protein search: BLASTX/DIAMOND search against NCBI nr
   • Nucleotide search: BLASTN search against NCBI core_nt
3. Low concern search: Clear earlier flags based on matches to common or conserved sequences

Information about the databases supporting screening can be found in the commec-databases repostiory.

Documentation

The GitHub Wiki has documentation for this package, including information about installing commec and interpreting screening results.

More information about the Common Mechanism project is available on the IBBIS project page and Common Mechanism FAQ.

Development

The commec package is being actively developed by IBBIS staff. We welcome contributions! To get started, install conda, and make sure that your channels are configured correctly. Then create the dev environment with:

conda env create -f environment.yml
conda activate commec-dev

From here, you should have an interactive version of the package installed via pip -e . and the necessary shell dependencies.