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full pipeline testing #6

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averagehat opened this issue Feb 25, 2016 · 1 comment
Open
1 of 4 tasks

full pipeline testing #6

averagehat opened this issue Feb 25, 2016 · 1 comment
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@averagehat
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Maybe sometime worth doing.

Read simulators:

related project: https://github.com/isovic/overlap-benchmark

these could go in bioconda but they are only a testing dependency and not a part of the framework so the user won't have to install

Data:

  • script to download reference from accession and mutate it etc.
  • blast database
@averagehat averagehat self-assigned this Feb 25, 2016
@necrolyte2 necrolyte2 added this to the Platform Read Simulation milestone Feb 25, 2016
@averagehat
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  • generate miseq from reference
  • generate pacbio from reference
  • mutation expected: 1043: A -> G, X%
  • Make/download reference
  • cut ref into X pieces, generate mutations on each piece
  • denovo/mapping

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