19 Oct 2017
On Thursday, October 19 at 11:00 a.m., join me at ASHG for a talk
about de novo assembly applied to MHC/HLA. This work examines
our current development version of Supernova(tm), the 10x Genomics
de novo assembler, specifically in the MHC region. For the samples
that we studied, MHC was in a single, phased scaffold. At the exon
level, the peptide binding sites were correctly reconstructed, to
base-level accuracy, for 35 of 36 genes x subjects. Most whole-genes
were reconstructed perfectly, with some genes having a small number
of putative subtitutions and indels.
more...
05 Apr 2017
Our paper describing Supernova, the 10x whole-genome de novo
assembler, is now available on-line (for free, thankfully) at
Genome Research. Supernova is unique in that it focuses on the generation
of diploid assemblies and is entirely turn-key. With proper input data, we
generate assemblies that are complete, contiguous, accurate, and phased.
As part of the validation of this paper, we assembled seven
genomes that are now available in GenBank. Feel free to email or say hi
on Twitter if you have questions.
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12 Feb 2016
So I will not be attending AGBT this year, however I’ve
spent the past 8 months working with David Jaffe on a new assembler
for 10X Genomics. David will be presenting this work in a
talk entitled
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23 Feb 2015
I’ll be talking at AGBT2015 about ``Personal Genome
Assembly.’’ This talk discusses how our group’s new version of
DISCOVAR, called DISCOVAR de novo, can be used to generate a
whole-genome assembly of very high quality, for about $10k in
sequencing and compute costs, all in.
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13 Nov 2014
Our group has a new paper out (advance publication) at Nature Genetics
called “Comprehensive variation discovery in single human genomes.”
This paper was the result of a ton of effort, of which mine is only a
part, and describes the earlier of our group’s two versions of the DISCOVAR
genome assembly algorithm.
more...