linkstream2 microblog

consensus method

http://www.biomedcentral.com/1471-2164/16/286/abstract

QT:{{”
We introduce GASVPro, an algorithm combining both paired read and read depth signals into a probabilistic model that can analyze multiple alignments of reads.
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http://genomebiology.com/2012/13/3/R22

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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. “}}

uses pacbio

http://bioinformatics.oxfordjournals.org/content/30/24/3458.long

Transduction of nonrepetitive DNA mediated by L1 retrotransposition in #cancer #genomes
http://www.sciencemag.org/content/345/6196/1251343.abs associated w/ hypomethylation

Jose M. C. Tubio1,
Yilong Li1,*,
Young Seok Ju1,*,
Inigo Martincorena1,
Susanna L. Cooke1,
…
Adrienne M. Flanagan30,31,
P. Andrew Futreal1,32,
Sam M. Janes3,
G. Steven Bova12,
Michael R. Stratton1,
Ultan McDermott1,
Peter J. Campbell1,10,33,‡

QT:{{”
Retrotransposons are DNA repeat sequences that are constantly on the move. By poaching certain cellular enzymes, they copy and insert themselves at new sites in the genome. Sometimes they carry along adjacent DNA sequences, a process called 3′ transduction. Tubio et al. found that 3′ transduction is a common event in human tumors. Because this process can scatter genes and regulatory sequences across the genome, it may represent yet another mechanism by which tumor cells acquire new mutations that help them survive and grow.
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http://www.nature.com/ncomms/2014/140205/ncomms4216/full/ncomms4216.html Mentioned as a mechanism for “occasional presence of templated insertions.”

It look as though the data are now ready for download
http://datasets.pacb.com/2013/Human10x/READS/index.html along with a brief description of the data
http://blog.pacificbiosciences.com/2013/10/data-release-long-read-shotgun.html

http://www.nature.com/nature/journal/v488/n7409/full/nature11284.html
Appears there’s germline variant calls (from JK) for potentially ~125 matched pairs