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.

Introduction

The Common Mechanism 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 screen command runs an input FASTA through four steps:

1. Biorisk scan (uses a hmmer search against custom databases)
2. Regulated protein scan (uses a BLASTX or DIAMOND search against NCBI nr)
3. Regulated nucleotide scan (uses BLASTN against NCBI nt)
4. Low-concern scan (uses hmmer, cmscan and BLASTN against custom databases)

The .screen.json file produced by that pipeline can be passed to flag to produce a convenient output CSV. The screen_pipeline_status.csv file has the following values:

Column Name	Type	Description
name	str	Name of screen file
filepath	path	Path to screen file
flag	status	Outcome of the overall screen
biorisk	status	Outcome of the biorisk search
protein	status	Outcome of the protein taxonomy search
nucleotide	status	Outcome of the nucleotide taxonomy search
cleared	status	Outcome of the low-concern search
virus_flag	bool	Did the taxonomy search flag sequences from a regulated virus?
bacteria_flag	bool	... or a regulated bacterial species?
eukaryote_flag	bool	... or a regulated eukaryotic (e.g. fungal) species?
cleared_protein	bool	Were any flags cleared by the low_concern protein search?
cleared_rna	bool	... or the low_concern RNA search?
cleared_dna	bool	... or the low_concern DNA search?

The flag column contains the overall recommendation is based on the following decision flow:

Documentation

The online documentation is located at the GitHub Wiki.

Development

Development dependencies are managed through a conda environment. Install conda, and make sure that your channels are configured correctly. Then create the 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 .) as well as the necessary shell dependencies.

About

The Common Mechanism is a project of IBBIS, the International Biosecurity and Biosafety Initiative for Science. From 2021-2023, the software and databases were developed by a team of technical consultants working with the Nuclear Threat Initiative, led by Dr. Nicole Wheeler of the University of Birmingham, and including contributions from Brittany Rife Magalis of the University of Louisville and Jennifer Lu of the Center for Computational Biology at Johns Hopkins University. In 2024, IBBIS became the home of the project