consensus method
Posts Tagged ‘1000sv’
Genome Biology | Full text | An integrative probabilistic model for identification of structural variation in sequencing data
May 4, 2015QT:{{”
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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Characterization of structural variants with single molecule and hybrid sequencing approaches
May 4, 2015QT:{{”
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
Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes
August 11, 2014Transduction 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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A Polymerase Theta-dependent repair pathway suppresses extensive genomic instability at endogenous G4 DNA sites : Nature Communications : Nature Publishing Group
May 11, 2014http://www.nature.com/ncomms/2014/140205/ncomms4216/full/ncomms4216.html Mentioned as a mechanism for “occasional presence of templated insertions.”
PacBio data for CHM1 genome
October 24, 2013It 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
Dissecting the genomic complexity underlying medulloblastoma : Nature : Nature Publishing Group
September 26, 2012http://www.nature.com/nature/journal/v488/n7409/full/nature11284.html
Appears there’s germline variant calls (from JK) for potentially ~125 matched pairs
linkstream2 microblog 