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 data sets from multiple sequencing technologies.  Data generated from SMRT^® Sequencing was subjected to assembly using different large-genome assemblers, and comparisons of the results will be shown.  These include results generated with HGAP, Celera^® Assembler, MIRA, PBJelly, and other assembly tools currently in development.  Improvements observed include a near 50% reduction in the number of contigs coupled with at least a doubling of contig N50 size 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.