text: user1769: 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?
  
  user73: 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.
  
original_text: 1769: <p>Working on various cancers I have an interest in detecting structural variation (SV) in human, we've successfully used various tools like <a href="http://gmt.genome.wustl.edu/packages/pindel/" rel="nofollow noreferrer">Pindel</a>, <a href="http://svdetect.sourceforge.net/Site/Home.html" rel="nofollow noreferrer">SVDetect</a>, <a href="https://github.com/Illumina/manta" rel="nofollow noreferrer">Manta</a>, and <a href="https://github.com/arq5x/lumpy-sv" rel="nofollow noreferrer">LUMPY</a>, to name a few for detecting SVs in illumina short-read sequencing.  I curious if anyone has successfully used ONTs <a href="https://nanoporetech.com/products/minion" rel="nofollow noreferrer">MinION</a> 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 <a href="https://github.com/fritzsedlazeck/Sniffles" rel="nofollow noreferrer">Sniffles</a>? </p>
  
  <p>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, <em>etc</em>?</p>
   73: <p>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:</p>
  
  <p><a href="https://community.nanoporetech.com/posts/breakout-structural-varia" rel="noreferrer">https://community.nanoporetech.com/posts/breakout-structural-varia</a></p>
  
  <p>Here are my attempts at grabbing non-creative chunks from those notes:</p>
  
  <ul>
  <li><p>Professor Wigard Kloosterman has been developing a bioinformatics pipeline called NanoSV for mapping genomic structural variants in patients with congenital abnormalities</p></li>
  <li><p>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]</p></li>
  <li><p>Dr. Sudha Rao from Genotypic Technology in India used the MinION sequencer with Sniffles for structural variation calling</p></li>
  </ul>
  
  <p>ONT have said that the sessions/talks from London Calling 2017 will all be made publicly available at some point in the future.</p>
  