July 7, 2019  |  

Whole-genome sequencing for comparative genomics and de novo genome assembly.

Authors: Benjak, Andrej and Sala, Claudia and Hartkoorn, Ruben C

Next-generation sequencing technologies for whole-genome sequencing of mycobacteria are rapidly becoming an attractive alternative to more traditional sequencing methods. In particular this technology is proving useful for genome-wide identification of mutations in mycobacteria (comparative genomics) as well as for de novo assembly of whole genomes. Next-generation sequencing however generates a vast quantity of data that can only be transformed into a usable and comprehensible form using bioinformatics. Here we describe the methodology one would use to prepare libraries for whole-genome sequencing, and the basic bioinformatics to identify mutations in a genome following Illumina HiSeq or MiSeq sequencing, as well as de novo genome assembly following sequencing using Pacific Biosciences (PacBio).

Journal: Methods in molecular biology
DOI: 10.1007/978-1-4939-2450-9_1
Year: 2015

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