Seven Major Trend Changes of 2013 - (i) Sequencing Technology
This commentary is our modest attempt to capture the essence of over 500 blog posts published here in 2013. A major trend change is defined as a situation, where the social perception morphed substantially between the beginning and the end of 2013.
1. Sequencing Technology - PacBio has Arrived
Researchers essentially gave up on PacBio technology by the end of 2012. Only two or three blogs covered it in positive light, ours being one of those. For example, readers may take a look at our following 2012 posts related to PacBio.
HDF5 Data Format for PacBio Sequences
Mixing Illumina and PacBio Data for Genome Finishing
Excellent Slides from Fisherman Lex on Combining PacBio and Short Reads
Basic Local Alignment with Successive Refinement (BLASR) for PacBio
HGAp Very Accurate de novo Genome Assembly from PacBio Data
PBSIM: PacBio reads simulator.
In contrast, the general perception among scientists was well captured by the concluding paragraph of a 2012 paper published in BMC Genomics.
The limited yield and high cost per base currently prohibit large scale sequencing projects on the Pacific Biosciences instrument. The PGM and MiSeq are quite closely matched in terms of utility and ease of workflow. The decision on whether to purchase one or the other will hinge on available resources, existing infrastructure and personal experience, available finances and the type of applications being considered.
Or by this satirical commentary from early 2012.
A new sequencing technology enters the ring: SHTseq(TM)
Longer Reads-Better Data noSHT (What would you do with 100Mb reads?).
We are able to generate super-long reads with our ARSesnsors. Using CrapBio- SHTseq technology we regularly get 10Mb reads and we have even seen reads of 100Mb which completely sequenced E. coli 20 times in a single read. Our base calling accuracy is 25%, but with genomes with extreme AT/GC bias it reaches 40%. Although this is lower than other platforms the longer reads allow you to extract much more information from our reads than old-fashioned 2nd generation sequencers. Also this error is totally randomly distributed (unlike homopolymer errors in other technologies!) and there is no decline in base calling accuracy toward the ends of reads. The last base in a read is just as good as the first base.
Cleaning up SHT with Illumina data
If, for whatever reason, you need accurate sequence data we have developed hybrid assembler that can incorporate Illumina error correcting reads. With our HybridAssemblyReadDenoisingSHT data you can simply upload you 100x illumina data with your sample and get reads returned to you will 99.999% accuracy*.
Fast forward by one year. The experts present at the #UCDAssemble workshop made the following forecast.
From ‘technology unsuitable for large-scale sequencing projects’ to ‘the only thing used to sequence bacterial genomes’ is a major shift in perception. Long reads have definitely arrived.
How did ‘extremely noisy’ PacBio reads turn out to be useful? Scientists started to realize that clean short reads also introduced noise through their short length, and that noise manifested into lower quality of assembly at the next level of analysis. So, they were trading one form of noise with another. The following two blog posts explained the above point in detail.
End of Short-Read Era? (Part I)
End of Short-Read Era? (Part II)
In other major sequencing technology-related shifts of 2013, (i) Illumina acquired Moleculo Inc. for longer read, (ii) Roche closed its 454 sequencing business and announced collaboration with PacBio, (iii) NabSys unveiled its instrument and (iv) Ion Torrent and BGI announced partnership with BGI buying 37 new Proton instruments.
Nanopore technology in general and Oxford Nanopore in particular continue to be the wildcards of the sequencing world. Lack of actual sequencing data from Oxford Nanopore has been a big complaint and the researchers perceive the company as ‘secretive’. Their patent submissions provides some insight into where the company is heading to.
Everything You Want to Know about Oxford Nanopore
Readers interested in staying ahead of the crowd regarding changing dynamics of sequencing world are encouraged to follow these excellent blogs.
Omics! Omics! by Keith Robison
In Between Lines of Code by Lex Nederbragt
Pathogens: Genes and Genomes by Nick Loman
