Methods for analyzing next-generation sequencing data VII. long-read assembly

Abstract

Long-read sequencing represented by Pacific Biosciences’ single-molecule real-time (SMRT) technology has been widely used for microbial genomes. We overview an analysis procedure of Lactobacillus hokkaidonensis LOOC260^T genome using the so-called “PacBio“ data. We describe (i) the characteristics of PacBio data, (ii) genome assembly using the HGAP program provided in the web-based NGS analysis tool called “DDBJ Pipeline”, (iii) the survey of assembled contigs such as quality scores and circularization. We also describe a typical strategy of finishing the circular contig (plasmid).