PhylOligo: A package to identify contaminant or untargeted organism sequences in genome assemblies

Abstract

Motivation Genome sequencing projects sometimes uncover more organisms than expected, especially for complex and/or non-model organisms. It is therefore useful to develop software to identify mix of organisms from genome sequence assemblies. Results Here we present PhylOligo, a new package including tools to explore, identify and extract organism-specific sequences in a genome assembly using the analysis of their DNA compositional characteristics. Availability and implementation The tools are written in Python3 and R under the GPLv3 Licence and can be found at https://github.com/itsmeludo/Phyloligo/. Contact ludovic.mallet@inra.fr Supplementary informationSupplementary dataare available at Bioinformatics online.