Integration of string and de Bruijn graphs for genome assembly | Zendy

YaoTing Huang | Zendy; Chen-Fu Liao | Zendy

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Integration of string and de Bruijn graphs for genome assembly

Author(s) -

YaoTing Huang,

Chen-Fu Liao

Publication year - 2016

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btw011

Subject(s) - de bruijn sequence , de bruijn graph , computer science , string (physics) , sequence assembly , graph , theoretical computer science , benchmark (surveying) , algorithm , biology , combinatorics , mathematics , genetics , gene , gene expression , transcriptome , geodesy , mathematical physics , geography

String and de Bruijn graphs are two graph models used by most genome assemblers. At present, none of the existing assemblers clearly outperforms the others across all datasets. We found that although a string graph can make use of entire reads for resolving repeats, de Bruijn graphs can naturally assemble through regions that are error-prone due to sequencing bias.

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