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Working on various cancers I have an interest in detecting structural variation (SV) in human, we've successfully used various tools like Pindel, SVDetect, Manta, and LUMPY, to name a few for detecting SVs in illumina short-read sequencing. I curious if anyone has successfully used ONTs MinION sequencer for detecting SV, as there are many cases where longer reads would be beneficial for SV detection especially where events are long and/or occur in repetitive regions. Has anyone tried or had success with tools previously designed for PacBio data such as Sniffles?

Supplementary question, obviously the MinION has not quite got the throughput of say the PacBio SEQUEL so can't generate low-pass coverage for the whole human genome as easily, has anyone got experience trying to generate reads targeting specific areas of the genome in areas that are known for translations, long inversions, duplications, etc?

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  • $\begingroup$ Since I last looked, it appears Sniffles now explicitly mentions MinION data as an input on it GitHub page. So that appears to be one tool which has been tried. $\endgroup$
    – Matt Bashton
    Commented Jun 4, 2017 at 13:21
  • $\begingroup$ What's your coverage? $\endgroup$
    – Manuel
    Commented Jun 4, 2017 at 14:36
  • $\begingroup$ We're planning to try a targeted approach in the first instance, but we're currently at planning stage, so I can't give you a figure as yet. $\endgroup$
    – Matt Bashton
    Commented Jun 4, 2017 at 16:07

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There was a Structural Variant breakout session at the London Calling conference this year. Unfortunately I didn't attend that session, but MinION community members have access to Constance Donnell's summary of that:

https://community.nanoporetech.com/posts/breakout-structural-varia

Here are my attempts at grabbing non-creative chunks from those notes:

  • Professor Wigard Kloosterman has been developing a bioinformatics pipeline called NanoSV for mapping genomic structural variants in patients with congenital abnormalities

  • Tomas Sesani at the University of Utah studied the precise copy number of duplicated genes in individual virus genes over time, and tracked the SNP within copy number variable regions of the genome [no public tool mentioned]

  • Dr. Sudha Rao from Genotypic Technology in India used the MinION sequencer with Sniffles for structural variation calling

ONT have said that the sessions/talks from London Calling 2017 will all be made publicly available at some point in the future.

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  • $\begingroup$ Thanks for this, yes it's often hard to figure out what software is out there for MinION related things as it ends up being posted behind the closed doors that only MinION community members have access too. This is an issue for bioinformatics people because the often won't have the account since they don't own the instrument. $\endgroup$
    – Matt Bashton
    Commented Jun 6, 2017 at 13:08

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