text: user2519: My professor in class said the following statements. 
  
  Short reads can map break points
  Long reads can disambiguate repeat related issues
  
  I'm very new to genomics, so I don't quite understand the first statement. What is meant by short reads can map break points. What are break points to begin with?
  
  user77: A "break point" typically denotes one end of a structural variation, such as an inversion or deletion. You can simply think of it as the position where the normal chromosome was broken to allow the variation. One can find these with short (Illumina) reads relatively easily since with paired end sequencing you'll have pairs spanning these breakpoints with odd relative orientations or insert sizes or such. Note that this is not a particular strength of short reads, since long reads are probably even better at this (they are not as good for finding SNPs at the moment though).
  
  user681: 
  Short reads can map break points
  
  With short reads you do an "indirect observation/inference" of a structural variant: based on your paired-end reads you figure out something is wrong because their distance or orientation is not what you expect. With long reads, you often get a direct observation of a breakpoint, with sufficient long reads on both sides (either split alignment or spanning the SV) allowing almost nucleotide accuracy. 
  
  Long reads can disambiguate repeat related issues
  
  Short reads cannot align unambiguously in many repetitive regions, because the repeat is longer than the read. Long reads, however, span most common repeats entirely, allowing you to unambiguously assign a location for each read, as such resolving the issues.
  
original_text: 2519: <p>My professor in class said the following statements. </p>
  
  <ol>
  <li>Short reads can map break points</li>
  <li>Long reads can disambiguate repeat related issues</li>
  </ol>
  
  <p>I'm very new to genomics, so I don't quite understand the first statement. What is meant by short reads can map break points. What are break points to begin with?</p>
   77: <p>A "break point" typically denotes one end of a structural variation, such as an inversion or deletion. You can simply think of it as the position where the normal chromosome was broken to allow the variation. One can find these with short (Illumina) reads relatively easily since with paired end sequencing you'll have pairs spanning these breakpoints with odd relative orientations or insert sizes or such. Note that this is not a particular strength of short reads, since long reads are probably even better at this (they are not as good for finding SNPs at the moment though).</p>
   681: <blockquote>
    <p>Short reads can map break points</p>
  </blockquote>
  
  <p>With short reads you do an "indirect observation/inference" of a structural variant: based on your paired-end reads you figure out something is wrong because their distance or orientation is not what you expect. With long reads, you often get a direct observation of a breakpoint, with sufficient long reads on both sides (either split alignment or spanning the SV) allowing almost nucleotide accuracy. </p>
  
  <blockquote>
    <p>Long reads can disambiguate repeat related issues</p>
  </blockquote>
  
  <p>Short reads cannot align unambiguously in many repetitive regions, because the repeat is longer than the read. Long reads, however, span most common repeats entirely, allowing you to unambiguously assign a location for each read, as such resolving the issues.</p>
  