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miComplete: weighted quality evaluation of assembled microbial genomes.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab. Max Planck Institute for Evolutionary Biology, Germany.ORCID iD: 0000-0002-0819-3359
Max Planck Institute for Evolutionary Biology, Germany.ORCID iD: 0000-0002-0098-1692
Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.ORCID iD: 0000-0001-8354-2398
2019 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, article id btz664Article in journal (Refereed) Epub ahead of print
Abstract [en]

SUMMARY: Metagenomics and single-cell genomics have revolutionized the study of microorganisms, increasing our knowledge of microbial genomic diversity by orders of magnitude. A major issue pertaining to metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) is to estimate their completeness and redundancy. Most approaches rely on counting conserved gene markers. In miComplete, we introduce a weighting strategy, where we normalize the presence/absence of markers by their median distance to the next marker in a set of complete reference genomes. This approach alleviates biases introduced by the presence/absence of shorter DNA pieces containing many markers, e.g. ribosomal protein operons.

AVAILABILITY AND IMPLEMENTATION: miComplete is written in Python 3 and released under GPLv3. Source code and documentation are available at https://bitbucket.org/evolegiolab/micomplete.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Place, publisher, year, edition, pages
2019. article id btz664
National Category
Bioinformatics (Computational Biology)
Research subject
Biology with specialization in Molecular Evolution
Identifiers
URN: urn:nbn:se:uu:diva-396617DOI: 10.1093/bioinformatics/btz664PubMedID: 31504158OAI: oai:DiVA.org:uu-396617DiVA, id: diva2:1368515
Funder
Carl Tryggers foundation , CTS 15:184Swedish Research Council, 2017-03709Available from: 2019-11-07 Created: 2019-11-07 Last updated: 2019-11-08Bibliographically approved

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