title: Whole-genome sequencing for comparative genomics and de novo genome assembly.
abstract: 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).
authors.affiliation: École polytechnique fédérale de Lausanne (EPFL), Global Health Institute, Lausanne, CH-1015, Switzerland.
authors.forename: Andrej
authors.initials: A
authors.lastname: Benjak
authors.forename: Claudia
authors.initials: C
authors.lastname: Sala
authors.forename: Ruben C
authors.initials: RC
authors.lastname: Hartkoorn
mesh_terms: D019295:Computational Biology / Q000379:methods; D016678:Genome; D016680:Genome, Bacterial; D015698:Genomic Library; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D009154:Mutation; D009169:Mycobacterium tuberculosis / Q000235:genetics