Hello Everyone,
We have been quiet while we have had our head down transitioning from a company with 2 sequencing platforms to a company with 4 sequencing platforms. That time has now passed. We don’t usually have posts focused on platforms as Cofactor has always been platform agnostic in order to match our platforms to each individual project. Also, platform posts are often akin to a craftsman highlighting the virtues of a new hammer… boring and what really matters is what can be accomplished with that hammer in the right hands. These new platforms are worth mention because their addition represents improvements in de-novo assembly projects and unprecedented project turnaround for smaller sequencing projects (to name a few).
First, let me introduce you to our first newcomer, the Roche 454 Junior. This machine operates in the same manner and read-length, using the same reagents, as the FLX machine. However, the output of machine is approximately 1/8 of a full 454 FLX run. Also, the price/run is on the order of 1/8 of an FLX run. This allows a researcher to perform several runs of amplicon sequencing with a decreased turnaround as compared to a normal 454 machine where a provider would need to get 7 other octets of clients prior to running the machine. In all honestly, this is not the main reason we brought in the machine, although a great one. The main reason is that we can sequence 10 and 20 kb long-insert mate pair libraries (to low physical coverage) for de novo assembly projects. We have fully adopted the multi-platform and library approach to de novo assemblies as highlighted in a paper published last Fall (1). The result, improved Illumina DNA and RNA de-novo assemblies.
Our second arrival is the Ion Torrent PGM unit. This is exciting because we now have a lower output and lower cost option better matched for miRNA-seq, ChIP-seq, and amplicon sequencing customers. This platform also has 3 hour run times compared to one week run times (Illumina and SOLiD standard runs) and allows us to better serve customers where project turnaround is key.
At this point, this makes us one of the only providers in the world running 4 of the most widely available next-generation sequencing platforms; Illumina, Applied Biosystems SOLiD, Roche 454, and Ion Torrent. These additions continue to support Cofactor scientists’ mission; Approaches and platforms chosen on the basis of scientist’s project goals to deliver key results at extraordinary value.
If you would like any further information concerning any of the developments mentioned above and how they relate to your project, please do not hesitate to contact me directly or email [email protected] for a quote from our team.
Happy Sequencing,
Jon Armstrong
Cofactor Genomics
1. PMID: 20386741
De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis.
Nowrousian, M., et. al. PLoS Genet. 2010 Apr 8;6(4):e1000891.
