Dataset Information

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

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.

SUBMITTER: Mallet L

PROVIDER: S-EPMC5860033 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Mallet Ludovic L Bitard-Feildel Tristan T Cerutti Franck F Chiapello Hélène H

Bioinformatics (Oxford, England) 20171001 20

<h4>Motivation</h4>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.<h4>Results</h4>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.<h4>Availability and implementatio ...[more]

PMID: 28637232

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Dataset Information

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

Motivation

Results

Availability and implementation

Contact

Supplementary information

Publications

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

Similar Datasets

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