Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data

• Published in: Microbial genomics Vol. 2; no. 8; p. e000083
• Main Authors: Page, Andrew J., De Silva, Nishadi, Hunt, Martin, Quail, Michael A., Parkhill, Julian, Harris, Simon R., Otto, Thomas D., Keane, Jacqueline A.
• Format: Journal Article
• Language: English
• Published: England Microbiology Society 01.08.2016
• Subjects: Genome, Bacterial - genetics; Genomics - economics; Genomics - methods; High-Throughput Nucleotide Sequencing; Methods Paper; Multilocus Sequence Typing; Prokaryotic Cells; Sequence Analysis, DNA - methods; Software; illumina; assembly; high-throughput; prokaryotic

The rapidly reducing cost of bacterial genome sequencing has lead to its routine use in large-scale microbial analysis. Though mapping approaches can be used to find differences relative to the reference, many bacteria are subject to constant evolutionary pressures resulting in events such as the lo...