BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics
Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying completeness of genomic data sets in terms of...
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Published in | Molecular biology and evolution Vol. 35; no. 3; pp. 543 - 548 |
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Main Authors | , , , , , , , |
Format | Journal Article |
Language | English |
Published |
United States
Oxford University Press
01.03.2018
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Subjects | |
Online Access | Get full text |
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Summary: | Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying completeness of genomic data sets in terms of the expected gene content of Benchmarking Universal Single-Copy Orthologs (BUSCO, http://busco.ezlab.org). The latest software release implements a complete refactoring of the code to make it more flexible and extendable to facilitate high-throughput assessments. The original six lineage assessment data sets have been updated with improved species sampling, 34 new subsets have been built for vertebrates, arthropods, fungi, and prokaryotes that greatly enhance resolution, and data sets are now also available for nematodes, protists, and plants. Here, we present BUSCO v3 with example analyses that highlight the wide-ranging utility of BUSCO assessments, which extend beyond quality control of genomics data sets to applications in comparative genomics analyses, gene predictor training, metagenomics, and phylogenomics. |
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Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 These authors are joint Second Authors. Present address: Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland Associate editor: Michael Rosenberg |
ISSN: | 0737-4038 1537-1719 |
DOI: | 10.1093/molbev/msx319 |