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Updated: Feb 28, 2026

Novel Sequence Discovery by Subtractive Genomics
Published on: January 25, 2019
PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies
Ludovic Mallet1, Tristan Bitard-Feildel2, Franck Cerutti1
1INRA UR875, Unité Mathématiques et Informatique Appliquées de Toulouse (MIAT), Auzeville, 31326 Castanet-Tolosan, France.
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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