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  miComplete: weighted quality evaluation of assembled microbial genomes

Hugoson, E., Lam, W. T., & Guy, L. (2019). miComplete: weighted quality evaluation of assembled microbial genomes. Bioinformatics, btz664. doi:10.1093/bioinformatics/btz664.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0004-EB9E-2 Version Permalink: http://hdl.handle.net/21.11116/0000-0005-1C9C-D
Genre: Journal Article

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 Creators:
Hugoson, Eric1, Author              
Lam, Wai Tin2, Author              
Guy, Lionel, Author
Affiliations:
1Research Group Microbial Molecular Evolution, Department Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_2497692              
2Department Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_2421699              

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 Abstract: 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.miComplete is written in Python 3 and released under GPLv3. Source code and documentation are available at https://bitbucket.org/evolegiolab/micomplete.Supplementary data are available at Bioinformatics online.

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Language(s): eng - English
 Dates: 2019-07-232019-04-132019-08-202019-08-222019-09
 Publication Status: Published in print
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 Identifiers: DOI: 10.1093/bioinformatics/btz664
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Title: Bioinformatics
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: - Sequence Number: btz664 Start / End Page: - Identifier: ISSN: 1367-4803
CoNE: https://pure.mpg.de/cone/journals/resource/954926969991