PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies.
basic_science · Level V
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- Record sourced from PubMed, PMID 28637232.
- Also identified by DOI 10.1093/bioinformatics/btx396 and PMC identifier 5860033.
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Abstract
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.
Medical subject headings
- Genomics
- Sequence Analysis, DNA
- Software