A Comparison of Assemblers and Strategies for Complex Large Genome Sequencing with PacBio® Long Reads

PacBio^® sequencing holds promise for addressing large genome complexities, such as long, highly repetitive, low complexity regions and duplication events that are difficult to resolve with short-read technologies.  Several strategies, with varying outcomes, are available for de novo sequencing and assembling of larger genomes.  Using a diploid fungal genome, estimated to be ~80 Mb in size, as the basis dataset for comparison, we highlight assembly options when using only PacBio sequencing or a combined strategy leveraging multiple sequencing technology data sets.  Comparisons of results generated from different assemblers available for large genome assembly using data generated from SMRT^® Sequencing will be shown.  These include results generated with HGAP, Celera, MIRA, PBJelly, and other assembly tools currently in development.  Improvements observed include a near 50% reduction in the number of contigs coupled with a doubling of contig N50 size, at the minimum, in genome assemblies incorporating SMRT^®sequencing data.  We further show how incorporating long reads also highlights new challenges and missed insights of short read assemblies arising from heterozygosity inherent in multiploid genomes.