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miComplete :
miComplete : weighted quality evaluation of assembled microbial genomes
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- Hugoson, Eric (författare)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab,Max Planck Institute for Evolutionary Biology, Germany
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- Lam, Wai Tin (författare)
- Max Planck Institute for Evolutionary Biology, Germany
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- Guy, Lionel, PhD, Docent, 1980- (författare)
- Uppsala universitet,Science for Life Laboratory, SciLifeLab,Institutionen för medicinsk biokemi och mikrobiologi
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(creator_code:org_t)
- 2019-08-22
- 2020
- Engelska.
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 36:3, s. 936-937
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Abstract
Ämnesord
Stäng
- 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.
Ämnesord
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
Nyckelord
- Biologi med inriktning mot molekylär evolution
- Biology with specialization in Molecular Evolution
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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