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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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
bioinformatics
Computer Science
computer software
DNA
Eukaryota - genetics
genome assembly
Genomics - methods
Mathematics
nucleotide sequences
Sequence Analysis, DNA - methods
Software
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cited_by cdi_FETCH-LOGICAL-c478t-43207760d59823fa9de15738d3ad6f6ef0335f524c6a908a25e46b99cbef8b3d3
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container_end_page 3285
container_issue 20
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container_title Bioinformatics (Oxford, England)
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creator Mallet, Ludovic
Bitard-Feildel, Tristan
Cerutti, Franck
Chiapello, Hélène
description 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.
doi_str_mv 10.1093/bioinformatics/btx396
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source Oxford Journals Open Access Collection; PubMed Central (PMC)
subjects Applications Notes
Bacteria - genetics
bioinformatics
Computer Science
computer software
DNA
Eukaryota - genetics
genome assembly
Genomics - methods
Mathematics
nucleotide sequences
Sequence Analysis, DNA - methods
Software
title PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies
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