Koala Pacific Chocolate assembly using Illumina short-read and BioNano optical mapping

Five libraries of PCR-free 250bp paired-end reads were produced on an Illumina HiSeq 2500. Each library gave approximately 20x coverage for the reported 3.5Gb genome of koala. Using Discovar, five different de novo assemblies were created using 21x, 43x, 64x, 85x and 107x coverage and assembly stats were established for each assembly.From the assembly calculations, 64x coverage assembly provided the best overall contiguity (and matched Discovar?s recommended 60x coverage) and hence this assembly was used for all subsequent analysis. The assembly had an estimated genome size of 3.165Gb (3.104Gb using 10Kb+ contigs) and an N50 of 308Kb. A hybrid assembly was then created, mapping the DISCOVAR assembly back to the restriction-site labelled BioNano molecules, resulting in increased N50 of 869Kb.