PacBio was a marked improvement compared to the Illumina-only assembly
Oklahoma Scientists Use SMRT Sequencing to Rescue Fungal Genome Assembly
(Tuesday, August 27, 2013) Scientists from Oklahoma State University and the University of Oklahoma teamed up with a sequencing service provider to study the genome of an anaerobic fungus found in the rumen of cows that may have implications for effective plant biomass degradation. What made this particular species so tricky to sequence were its extreme GC content — just 17 percent — and unusually high number of repeats.
These remarkable insights were attained by a two-part attempt to sequence the organism’s genome. As described in the paper, the team initially used paired-end sequencing on the Illumina platform to generate an assembly with 290-fold coverage that was “highly fragmented … with an extremely large number of contigs in the final assembly (82,325 contigs), a large proportion of the final assembly (32.4%) harbored in extremely short contigs (300 to 900 bp), and a low N50 (1,666 bp).”
So Elshaheda et al. turned to SMRT® Sequencing, generating about 10-fold coverage of the C1A isolate. PacBioToCA was used to produce a hybrid assembly of the fungus that had an average quality score of 59.7. “The final assembly was a marked improvement compared to the Illumina-only assembly, as evident from the improved N50/N90 values” and other characteristics, the authors write. They note that the long PacBio reads “allowed for the identification of a large number of introns previously undetected in the Illumina assembly.”