De novo assembly and genotyping of variants using colored de Bruijn graphs
Detecting genetic variants that are highly divergent from a reference sequence remains a major challenge in genome sequencing. We introduce de novo assembly algorithms using colored de Bruijn graphs for detecting and genotyping simple and complex genetic variants in an individual or population. We p...
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| Format: | Online |
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2012
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272472/ |
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pubmed-32724722012-08-01 De novo assembly and genotyping of variants using colored de Bruijn graphs Iqbal, Zamin Caccamo, Mario Turner, Isaac Flicek, Paul McVean, Gil Article Detecting genetic variants that are highly divergent from a reference sequence remains a major challenge in genome sequencing. We introduce de novo assembly algorithms using colored de Bruijn graphs for detecting and genotyping simple and complex genetic variants in an individual or population. We provide an efficient software implementation, Cortex; the first de novo assembler capable of assembling multiple eukaryote genomes simultaneously. Four applications of Cortex are presented. First, we detect and validate both simple and complex structural variation in a high coverage human genome. Second, we identify over 3Mb of novel sequence in pooled low-coverage population sequence data from the 1000 Genomes Project. Third, we show how population information from 10 chimpanzees enables accurate variant calls without a reference sequence. Finally, we estimate classical HLA genotypes at HLA-B, the most variable gene in the human genome. 2012-01-08 /pmc/articles/PMC3272472/ /pubmed/22231483 http://dx.doi.org/10.1038/ng.1028 Text en Users may view, print, copy, download and text and data- mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Iqbal, Zamin Caccamo, Mario Turner, Isaac Flicek, Paul McVean, Gil |
| spellingShingle |
Iqbal, Zamin Caccamo, Mario Turner, Isaac Flicek, Paul McVean, Gil De novo assembly and genotyping of variants using colored de Bruijn graphs |
| author_facet |
Iqbal, Zamin Caccamo, Mario Turner, Isaac Flicek, Paul McVean, Gil |
| author_sort |
Iqbal, Zamin |
| title |
De novo assembly and genotyping of variants using colored de Bruijn graphs |
| title_short |
De novo assembly and genotyping of variants using colored de Bruijn graphs |
| title_full |
De novo assembly and genotyping of variants using colored de Bruijn graphs |
| title_fullStr |
De novo assembly and genotyping of variants using colored de Bruijn graphs |
| title_full_unstemmed |
De novo assembly and genotyping of variants using colored de Bruijn graphs |
| title_sort |
de novo assembly and genotyping of variants using colored de bruijn graphs |
| description |
Detecting genetic variants that are highly divergent from a reference sequence remains a major challenge in genome sequencing. We introduce de novo assembly algorithms using colored de Bruijn graphs for detecting and genotyping simple and complex genetic variants in an individual or population. We provide an efficient software implementation, Cortex; the first de novo assembler capable of assembling multiple eukaryote genomes simultaneously. Four applications of Cortex are presented. First, we detect and validate both simple and complex structural variation in a high coverage human genome. Second, we identify over 3Mb of novel sequence in pooled low-coverage population sequence data from the 1000 Genomes Project. Third, we show how population information from 10 chimpanzees enables accurate variant calls without a reference sequence. Finally, we estimate classical HLA genotypes at HLA-B, the most variable gene in the human genome. |
| publishDate |
2012 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272472/ |
| _version_ |
1611503795523551232 |