In the past, the major attention of algorithm developers working on long noisy reads (Pacbio, Nanopore) had been directed to noise correction and genome assembly. Now that the costs have come down, users are looking into other applications, including finding SNPs.
Investor warning: The following post is for entertainment purposes only, and should not be considered as financial advice of any sort.
In Feb 2016, we made a forecast that Oxford Nanopore would go out of business by the end of 2017. That did not happen, and we do deserve to get an ‘F’ for that forecast. We would also like to take this opportunity to make our readers aware of a relevant (and highly controversial) investment research report that came out recently.
Yesterday, Pacbio received its Christmas present for 2016. Roche decided to abruptly terminate its
three year-long alliance with the company. During this collaboration, Roche paid Pacbio to develop the Sequel instrument and
reserved the exclusive right to sell it in the human clinical market.
Investor warning: The following post is for entertainment purpose only, and should not be considered as financial advice of any sort. Please consult your favorite government-certified investment adviser or central banker regarding decisions on investing your life savings.
Readers may keep an eye on #SMRTBFX hashtag on twitter to follow an ongoing conference. This is the best place to know about the latest bioinformatics algorithms on long reads.
Gene Myers is again the star of the show. He has been distributing a lot of goodies through his Dazzlerblog, such as -
David Eccles, who provides excellent
update on the latest advances related to Oxford Nanopore technology,
pointed out that two new open source base-callers have been released last
week. So far the researchers relied on the proprietary software provided by
Oxford Nanopore, and that required having internet connection in remote
locations. It is also noteworthy that at least the second paper claims to
improve basecalling accuracy (“By employing carefully crafted recurrent neural
networks, our tool improves the base calling accuracy compared to the default
base caller supplied by the manufacturer.”). Overall, these are very exciting
times in the sequencing world.
Investor warning: The following post is for entertainment purpose only, and should not be considered as financial advice of any sort. Please consult your favorite government-certified investment adviser or central banker to decide, where to invest your life savings.
A few months, we wrote about Heng Li’s Minimap and
Miniasm. Yesterday, Mark
Chaisson posted a chart in twitter showing that they perform really well for
assembling pacbio reads. Miniasm is excellent even with low coverage.
Suppose you can locate a long read in the tardigrade genome sequencing data
that has three genes from bacteriodes and three from tardigrade. Is that
convincing evidence that microbial genes got integrated into the tardigrade
genome through horizontal gene transfer?
Shengfeng Huang, the author of HaploMerger, informed us about the release of
HaploMerger2 built with new and improved algorithm. Those working on assembly
of heterozygous genomes should give it a try.
We like to alert our readers about a new blog post from Gene Myers on assembly
of Pacbio reads. In it, Myers wrote about his frustration with incorporating
quality scores coming out the machines -
