Meta-IDBA: a de Novo assembler for metagenomic data | Zendy

Yu Peng | Zendy; Henry C. M. Leung | Zendy; SiuMing Yiu | Zendy; Francis Y. L. Chin | Zendy

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Meta-IDBA: a de Novo assembler for metagenomic data

Author(s) -

Yu Peng,

Henry C. M. Leung,

SiuMing Yiu,

Francis Y. L. Chin

Publication year - 2011

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/btr216

Subject(s) - metagenomics , contig , de bruijn graph , genome , bottleneck , sequence assembly , computational biology , biology , subspecies , reference genome , de bruijn sequence , computer science , graph , genetics , theoretical computer science , gene , mathematics , ecology , combinatorics , gene expression , transcriptome , embedded system

Next-generation sequencing techniques allow us to generate reads from a microbial environment in order to analyze the microbial community. However, assembling of a set of mixed reads from different species to form contigs is a bottleneck of metagenomic research. Although there are many assemblers for assembling reads from a single genome, there are no assemblers for assembling reads in metagenomic data without reference genome sequences. Moreover, the performances of these assemblers on metagenomic data are far from satisfactory, because of the existence of common regions in the genomes of subspecies and species, which make the assembly problem much more complicated.

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