Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT
Abstract Current-day metagenomics analyses increasingly involve de novo taxonomic classification of long DNA sequences and metagenome-assembled genomes. Here, we show that the conventional best-hit approach often leads to classifications that are too specific, especially when the sequences represent...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2019-10-01
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| Series: | Genome Biology |
| Online Access: | http://link.springer.com/article/10.1186/s13059-019-1817-x |
| _version_ | 1818980741792399360 |
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| author | F. A. Bastiaan von Meijenfeldt Ksenia Arkhipova Diego D. Cambuy Felipe H. Coutinho Bas E. Dutilh |
| author_facet | F. A. Bastiaan von Meijenfeldt Ksenia Arkhipova Diego D. Cambuy Felipe H. Coutinho Bas E. Dutilh |
| author_sort | F. A. Bastiaan von Meijenfeldt |
| collection | DOAJ |
| description | Abstract Current-day metagenomics analyses increasingly involve de novo taxonomic classification of long DNA sequences and metagenome-assembled genomes. Here, we show that the conventional best-hit approach often leads to classifications that are too specific, especially when the sequences represent novel deep lineages. We present a classification method that integrates multiple signals to classify sequences (Contig Annotation Tool, CAT) and metagenome-assembled genomes (Bin Annotation Tool, BAT). Classifications are automatically made at low taxonomic ranks if closely related organisms are present in the reference database and at higher ranks otherwise. The result is a high classification precision even for sequences from considerably unknown organisms. |
| first_indexed | 2024-12-20T17:20:15Z |
| format | Article |
| id | doaj.art-e2f82306a2f447aca0d7da181b561e44 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-20T17:20:15Z |
| publishDate | 2019-10-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-e2f82306a2f447aca0d7da181b561e442022-12-21T19:31:51ZengBMCGenome Biology1474-760X2019-10-0120111410.1186/s13059-019-1817-xRobust taxonomic classification of uncharted microbial sequences and bins with CAT and BATF. A. Bastiaan von Meijenfeldt0Ksenia Arkhipova1Diego D. Cambuy2Felipe H. Coutinho3Bas E. Dutilh4Theoretical Biology and Bioinformatics, Science for Life, Utrecht UniversityTheoretical Biology and Bioinformatics, Science for Life, Utrecht UniversityTheoretical Biology and Bioinformatics, Science for Life, Utrecht UniversityCentre for Molecular and Biomolecular Informatics, Radboud University Medical CentreTheoretical Biology and Bioinformatics, Science for Life, Utrecht UniversityAbstract Current-day metagenomics analyses increasingly involve de novo taxonomic classification of long DNA sequences and metagenome-assembled genomes. Here, we show that the conventional best-hit approach often leads to classifications that are too specific, especially when the sequences represent novel deep lineages. We present a classification method that integrates multiple signals to classify sequences (Contig Annotation Tool, CAT) and metagenome-assembled genomes (Bin Annotation Tool, BAT). Classifications are automatically made at low taxonomic ranks if closely related organisms are present in the reference database and at higher ranks otherwise. The result is a high classification precision even for sequences from considerably unknown organisms.http://link.springer.com/article/10.1186/s13059-019-1817-x |
| spellingShingle | F. A. Bastiaan von Meijenfeldt Ksenia Arkhipova Diego D. Cambuy Felipe H. Coutinho Bas E. Dutilh Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT Genome Biology |
| title | Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT |
| title_full | Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT |
| title_fullStr | Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT |
| title_full_unstemmed | Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT |
| title_short | Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT |
| title_sort | robust taxonomic classification of uncharted microbial sequences and bins with cat and bat |
| url | http://link.springer.com/article/10.1186/s13059-019-1817-x |
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