De Novo Genome Assembly from DNA-Seq

DNA-Seq libraries were prepared from fragmented DNA (COVARIS S2, Woburn, Massachusetts, USA) according to recommendations made by the supplier (TruSeq DNA sample preparation v2 guide, Illumina, San Diego, CA, USA). Libraries were quantified by fluorometry, immobilised and processed onto a flow cell with a cBot followed by sequencing by synthesis by applying TruSeq v3 chemistry on a HiSeq2500 (all components by Illumina).
The de novo assembly of the reads was performed in CLC Genomics Workbench 7.0 (http://www.clcbio.com). The assembly data was exported as a BAM file, indexed using SAMtools [47 (link)] and imported in Gap5 [48 (link)]. Gaps were closed by PCR and primer-walking by applying dye-terminator sequencing performed on an ABI 310 capillary sequencer (Life technologies, Carlsbad, CA, USA).