IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth | Zendy

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

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IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

Author(s) -

Yu Peng,

Henry C. M. Leung,

SiuMing Yiu,

Francis Y. L. Chin

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/bts174

Subject(s) - contig , metagenomics , de bruijn graph , sequence assembly , hybrid genome assembly , computer science , dna sequencing , k mer , deep sequencing , genome , computational biology , reference genome , de bruijn sequence , nanopore sequencing , biology , algorithm , graph , genetics , theoretical computer science , mathematics , gene , gene expression , transcriptome , discrete mathematics

Next-generation sequencing allows us to sequence reads from a microbial environment using single-cell sequencing or metagenomic sequencing technologies. However, both technologies suffer from the problem that sequencing depth of different regions of a genome or genomes from different species are highly uneven. Most existing genome assemblers usually have an assumption that sequencing depths are even. These assemblers fail to construct correct long contigs.

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