Japanese Journal of Lactic Acid Bacteria
Online ISSN : 2186-5833
Print ISSN : 1343-327X
ISSN-L : 1343-327X
Review
Methods for analyzing next-generation sequencing dataVI. genome assembly
Yasuhiro TanizawaEli KaminumaYasukazu NakamuraKentaro ShimizuKoji Kadota
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2016 Volume 27 Issue 1 Pages 41-52

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Abstract

Genome assembly is a major task of NGS analyses. For this purpose, many assemblers based on the de Bruijn graph have been developed. In the framework, each node represents a series of overlapping k-mers (k nucleotides) and contigs can be obtained as paths solved from the k-mer graph. The most significant parameter is therefore k. We overview conventional approaches for de novo assembly of bacterial genomes. We first describe a command-line based NGS analysis pipeline on Bio-Linux: (1) the characteristics of Illumina MiSeq data using the quality check program FastQC, (2) adapter trimming using FaQCs, (3) de novo assembly using Velvet with different k-mers, (4) estimation of genome size using KmerGenie, and (5) filtering short sequences using an in-house Python program. We next describe the web-based NGS analysis tool called “DDBJ Pipeline”, taking two major assemblers (Velvet and Platanus) for instance. We discuss the effect of different k-mers on assembly results using Velvet and the difference between Velvet and Platanus.

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© 2016 Japan Society for Lactic Acid Bacteria
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