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

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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 information

Supplementary data are available at Bioinformatics online.

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