2015: The Year of Long Reads?

Posted on March 19, 2015 by Alex

We couldn’t help noticing that "long reads" kept popping up in presentations and posters at AGBT, and we certainly weren’t alone. Aside from longtime long-read provider Pacific Biosciences and synthetic long-read service Moleculo, acquired by Illumina in 2012, new companies such as 10X Genomics and Dovetail Genomics were touting the value of this kind of information at AGBT.

We’re already seeing sessions on long-read sequencing on the agendas of other upcoming conferences, leading to our theory that 2015 will go down in sequencing history as the Year of Long Reads. It’s no wonder demand for this kind of data is soaring: after years of using short-read sequencers to analyze genomes, scientists are just now realizing how much information about structural variants, haplotype phasing, and other long-range, clinically relevant elements is inaccessible with short reads alone.

There are a couple of different approaches to long-read data. Single-molecule sequencing platforms, like those available through PacBio and Oxford Nanopore Technologies, generate truly long reads on their own. Users of both platforms have presented individual reads running well into tens of kilobases, a far cry from the few hundred bases we’re used to from Illumina and Ion Torrent sequencers. Assembling those long reads can lead to megabase-plus contigs.

But since the vast majority of sequencing data currently available has been produced with short-read technologies, there’s also a huge appetite for bolt-on products that can pull long-range information out of short-read data. Like their older sibling Moleculo, upstarts 10X Genomics and Dovetail Genomics focus on altering library prep in a short-read workflow to allow analytical tools to connect the sequence data into much longer blocks. These synthetic long reads have been shown to elucidate larger elements like structural variants without switching sequencing platforms.

Both approaches suggest an exciting trend that will let us get more out of each genome we sequence. Here at Sage Science, we’re pleased to report that our BluePippin automated DNA size selection platform can be used with either of these approaches to maximize the length of reads generated or synthesized. For an example of how BluePippin works with synthetic reads, check out this blog post; learn more about BluePippin with long-read sequencing in these app notes. And check back soon for new info on how the PippinHT can be used with long-read workflows too!

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