What Strategy and how much Coverage is Needed for Bacterial de novo Sequencing?
In the NGS (Next Generation Sequencing) group of the networking platform LinkedIn I came across a lively discussion about the best strategy for de novo sequencing of a bacterial genome. The discussion was about technology (Roche versus Illumina), coverage (from 10-fold on Roche GS FLX to 500-fold on Illumina HiSeq 2000) and library types. The comments and advices given coincide with our experience that this question can not be answered without any further information on the genome to be sequenced. GC content, amount and size of repeat structures as well as the genome size of the bacterium have to be considered. We have meanwhile de novo sequenced more than 100 microbial genomes and according to our experience GS FLX technology with a combination of shotgun and long paired end libraries will deliver a high quality genome sequence that is suitable for gap closing projects.