Is the Era of Short Reads and de Bruijn Assembly Over?

Even though Oxford Nanopore did not come back to AGBT this year, other presentations suggest that long reads are back in vogue. The usual culprits - PacBio and Moleculo - seem to be carrying the torch. We have not gone through all discussions yet, but readers may take a look at PacBio Blog and this article - “A coming of age for PacBio and long read sequencing? #AGBT13” for useful information.

Our reader Jason Chin of PacBio presented a highly informative poster on his HGap assembly algorithm, but we did not find a public source from where it can be downloaded.

Edit. Here is Chen-Shan’s poster (click on image to get to pdf):

Edit.

Omics! Omics! blog provides very good perspective PacBio vs Moleculo, as well as on where the major future challenges lie.

Post AGBT: A Longish Item on Long Sequencing

For application space, most examples given at AGBT were either genome assembly (including gap filling and other improvements), structural variant discovery and haplotyping. One poster showed the use of PacBio for cDNA sequencing, which will certainly be a boon to cataloging splice variants. Metagenomics applications came up in Q&A;, but I dont believe any talks or posters actually showed this.