Can anybody suggest how much pacbio coverage do we need for a genome of 1.7 giga bases (de novo assembly)? We already have about 47X illumina reads (paired end, mate pairs 9 and 11 Kb) and the assembly that we generated is not so great (scaffold N50 of 36Kb, but 50% Ns). Most importantly, the genome has ~50% repeat content. We have a shared budget that we need to split for both pacbio DNA sequencing and Iso-seq (for future genome annotation: this spp doesn't have any transcriptome data). What do you guys think is the ideal coverage we need aim for to get a quality assembly?
Any suggestions on this will be greatly appreciated!