CodingDiv: analyzing SNP-level microdiversity to discriminate between coding and noncoding regions in viral genomes

Abstract

Summary Viral genes, that are frequently small genes and/or with large overlaps, are still difficult to predict accurately. To help in exhaustive gene prediction of viral genomes, we provide CodingDiv that detects SNP-level microdiversity of all potential coding regions, using metagenomic reads and/or similar sequences from external databases. Protein coding regions can then be identified as the ones containing more synonymous SNPs than unfavorable non-synonymous substitutions SNPs. Availability CodingDiv is released under the GPL license. Source code is available at https://github.com/ericolo/codingDiv. The software can be installed and used through a docker container. Supplementary information Supplementary data are available at Bioinformatics online.