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Project 8: Explore the use of 10x Genomics' Linked-Reads to unlock currently inaccessible parts of the genome #3

Open ttimbers opened 8 years ago

ttimbers commented 8 years ago

Project: 10x Genomics (http://software.10xgenomics.com/) has developed a technology that produces new type of long-range sequencing data called Linked-Reads. Long (>100Kb) double stranded DNA is separated into millions of droplets, from which barcoded short-read libraries are produced. This produces sequencing libraries that are sequence-able on standard short-read sequencers, but which provide long-range information that is completely lost in standard short-read libraries. These barcoded short-reads, which can be traced back to their original long starting DNA molecules, are called Linked-Reads. Linked-Reads enable applications impossible with short-reads including diploid rather than haploid, resolution of mutation calls (i.e. phasing), high quality structural variation calling, true diploid de novo assembly, and the unlocking of parts of the genome that cannot be accurately assayed with short-read technologies. For this proposed project, we will explore use of Linked-Reads to unlock biologically and clinically important variants parts of the genome for which existing (i.e. pre-Linked-Read) technologies have been totally inadequate. The project will require developing novel algorithms and building upon algorithms that have already been built by 10x Genomicsäó» and customers to take full advantage of the long-range information contained in Linked-Reads.

Project lead: Michael Schnall-Levin / @mike10x / Industry Professional / 10x Genomics

sjackman commented 8 years ago

We're planning to have a Docker image with a bunch of bioinformatics software preinstalled running on machines at the BC Cancer Agency Genome Sciences Centre during the Hackathon. Which bioinformatics software do you plant to use for your project? In particular, is there any software that you plan to use that is not already listed here? http://www.bcgsc.ca/services/orca

sauloal commented 8 years ago

https://sourceforge.net/projects/fragscaff/files/ - for 10 scaffolding

sjackman commented 8 years ago

Ah, so fragScaff does work with 10x data. Do you have a short tutorial of how to set the parameters of fragScaff appropriately for 10x data? I'll add it to Homebrew-Science and the Docker image.

aquaskyline commented 7 years ago

@sjackman Is the tutorial available? I'm using fragScaff on 10x data and I wonder how to let fragScaff know the barcode grouping of 10x reads.

sjackman commented 7 years ago

Hi, Ruibang. I haven't run fragScaff myself, but you may want to try out a similar tool from our lab, ARCS: https://github.com/bcgsc/arcs http://biorxiv.org/content/early/2017/01/17/100750

aquaskyline commented 7 years ago

This comes just in time, thanks Shaun!