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

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. Here we present PhylOligo, a new package including tools to explore,...

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Bibliographic Details
Published in:Bioinformatics (Oxford, England) England), 2017-10, Vol.33 (20), p.3283-3285
Main Authors: Mallet, Ludovic, Bitard-Feildel, Tristan, Cerutti, Franck, Chiapello, Hélène
Format: Article
Language:English
Subjects:
Applications Notes
Bacteria - genetics
Computer Science
Eukaryota - genetics
Genomics - methods
Mathematics
Sequence Analysis, DNA - methods
Software
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Summary: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. 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. The tools are written in Python3 and R under the GPLv3 Licence and can be found at https://github.com/itsmeludo/Phyloligo/. ludovic.mallet@inra.fr. Supplementary data are available at Bioinformatics online.
ISSN:1367-4803
1367-4811
DOI:10.1093/bioinformatics/btx396