Long Noisy Reads

Finding SNPs from Long Noisy Reads

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.

A New Nemesis for Nanopore

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.

Roche Dumps Pacbio

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.

Business analysis - Oxford Nanopore

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.

Ongoing Pacbio bioinformatics meeting (#SMRTBFX)

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 -

Single-Molecule Protein Identification by Sub-Nanopore Sensors

Sequencing That Stimulates The Sensors (Fascinating Ted Talk by David Eccles)

Accurate selfcorrection of errors in long reads using de Bruijn graphs

Nanopore - Two New Basecallers Released

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.

Minimap and Miniasm Paper is out

Our #AGBT16 Forecast - Oxford Nanopore Will Go Out of Business by 2017

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.

Live Streaming of Pacbio Session at #AGBT16

You will enjoy a number of very good talks on the Sequel system.

Pacbio Assembly - Miniasm Works Best (Chaisson)

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.

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

Chimeric Pacbio Reads and Tardigrade Controversy

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?

Cost of Human-sized Genome Sequencing with PacBio Sequel

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Please Try New and Polished HaploMerger2 for Assembly of Heterozygous Genomes

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.

New Blog Post from Gene Myers on "Intrinsic Quality Values" of Pacbio Sequences

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 -

JGI Researchers on The Economics of New PacBio Instrument

A month back, Pacbio announced the new instrument and we wrote -

New Paper from Nanopore (ONT) Consortium Submitted in F1000

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