linkstream2 microblog

We’re now all ILLUMINATED: DNA Sequencing Giant $ILMN Will Buy @PacBio For $1.2B, by @MatthewHerper
https://www.Forbes.com/sites/matthewherper/2018/11/01/dna-sequencing-giant-illumina-will-buy-pacific-biosciences-for-12-billion–exclusive-ceo-interview/ After raising $360M from VCs + $200M from an IPO

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“Pacific Biosciences was originally supposed to be an Illumina-killer. Founded in 2003 by chief technology officer, Steven Turner, who invented the firm’s basic technology with PacBio’s chief scientific officer, Jonas Korlach, PacBio emerged in 2009 boasting that it would disrupt the sequencing market, raising $360 million in venture capital and scoring a $200 million initial public offering. But its machines were too slow, expensive and unwieldy to slow down Illumina’s ascent. Shares plummeted, and even at the rich premium being offered by Illumina, shares are at half the IPO price.”
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LongISLND: in silico sequencing of lengthy & noisy datatypes https://www.ncbi.nlm.nih.gov/pubmed/27667791 @PacBio sim. software (NB: was advisor to @binaTechs)

Characterization of #SVs w. single molecule & hybrid sequencing http://bioinformatics.oxfordjournals.org/content/30/24/3458.abstract Probabilistic read mapping, re-evaluating adjacencies

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We present MultiBreak-SV, an algorithm to detect structural variants
(SVs) from single molecule sequencing data, paired read sequencing
data, or a combination of sequencing data from different platforms.
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http://biorxiv.org/content/early/2014/08/14/008003

http://blog.pacificbiosciences.com/2014/02/data-release-54x-long-read-coverage-for.html

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We are pleased to make publicly available a new shotgun sequence dataset of long PacBio® reads from a human DNA sample. We previously released sequence data using Single Molecule, Real-Time (SMRT®) Sequencing of ~10x coverage of this sample, sufficient for
reference-based detection of structural variation. Today we expand on that release with additional data that increases the total sequencing coverage to ~54x. This long-read data has enabled the generation of the first de novohuman genome assembly from PacBio-only sequence reads. Download the 54x long-read coverage dataset.

The dataset was generated from sequencing a well-studied human cell line (CHM1htert), which is being utilized as part of a National Institutes of Health project to sequence and assemble an alternate reference genome (the “platinum genome”). This NIH project is being led by Rick Wilson from Washington University at St. Louis and Evan Eichler from the University of Washington in collaboration with investigators from the National Center for Biotechnology Information. “}}

Characterization of the… #transcriptome by hybrid sequencing, using Illumina reads to error-correct #PacBio ones
http://www.pnas.org/content/110/50/E4821.long