De novo detection of copy number variation by co-assembly | Zendy

Jurgen F. Nijkamp | Zendy; Marcel A. van den Broek | Zendy; Jan-Maarten A. Geertman | Zendy; Marcel J. T. Reinders | Zendy; JeanMarc Daran | Zendy; Dick de Ridder | Zendy

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De novo detection of copy number variation by co-assembly

Author(s) -

Jurgen F. Nijkamp,

Marcel A. van den Broek,

Jan-Maarten A. Geertman,

Marcel J. T. Reinders,

JeanMarc Daran,

Dick de Ridder

Publication year - 2012

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/bts601

Subject(s) - contig , sequence assembly , copy number variation , genome , reference genome , biology , computational biology , computer science , dna sequencing , genomics , genetics , enumeration , copy number analysis , mathematics , gene , combinatorics , gene expression , transcriptome

Comparing genomes of individual organisms using next-generation sequencing data is, until now, mostly performed using a reference genome. This is challenging when the reference is distant and introduces bias towards the exact sequence present in the reference. Recent improvements in both sequencing read length and efficiency of assembly algorithms have brought direct comparison of individual genomes by de novo assembly, rather than through a reference genome, within reach.

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