ArticleBioinformatics (Oxford, England)2017
PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Contamination of fungal genomes of Onygenaceae (Phylum Ascomycota) in public databases: incidence, detection, and impact.BMC genomics · 2025Article
- Highly resolved genome assembly and comparative transcriptome profiling reveal genes related to developmental stages of tapewormProceedings. Biological sciences · 2024Article
- ContScout: sensitive detection and removal of contamination from annotated genomes.Nature communications · 2024Article
- Genome Assembly and Population Sequencing Reveal Three Populations and Signatures of Insecticide Resistance of Tuta absoluta in Latin America.Genome biology and evolution · 2023Article
- Contamination detection in genomic data: more is not enough.Genome biology · 2022Review
- Music of metagenomics-a review of its applications, analysis pipeline, and associated tools.Functional & integrative genomics · 2022Review
- Draft Genome Sequences of Thelohania contejeani and Cucumispora dikerogammari, Pathogenic Microsporidia of Freshwater Crustaceans.Microbiology resource announcements · 2021Article
- The Genome of the Blind Soil-Dwelling and Ancestrally Wingless Dipluran Campodea augens: A Key Reference Hexapod for Studying the Emergence of Insect Innovations.Genome biology and evolution · 2020Article
- A demonstration of unsupervised machine learning in species delimitation.Molecular phylogenetics and evolution · 2019Article
- A High-quality Draft Genome Assembly of Sinella curviseta: A Soil Model Organism (Collembola).Genome biology and evolution · 2019Article
- Article
- Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains.BMC genomics · 2018Article
- Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationGenome 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.
resultsHere 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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.