Benjak Andrej, Sala Claudia, Hartkoorn Ruben C
École polytechnique fédérale de Lausanne (EPFL), Global Health Institute, Lausanne, CH-1015, Switzerland.
Methods Mol Biol. 2015;1285:1-16. doi: 10.1007/978-1-4939-2450-9_1.
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).
用于分枝杆菌全基因组测序的新一代测序技术正迅速成为比更传统测序方法更具吸引力的替代方案。特别是，这项技术已证明可用于分枝杆菌突变的全基因组鉴定（比较基因组学）以及全基因组的从头组装。然而，新一代测序会产生大量数据，只有使用生物信息学才能将其转化为可用且可理解的形式。在这里，我们描述了用于全基因组测序文库制备的方法，以及在Illumina HiSeq或MiSeq测序后鉴定基因组突变的基本生物信息学方法，以及使用太平洋生物科学公司（PacBio）测序后的基因组从头组装方法。
