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Use spades#3

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martinghunt merged 10 commits intosanger-pathogens:mastersanger-pathogens/ariba:masterfrom martinghunt:use_spadesmartinghunt/ariba:use_spadesCopy head branch name to clipboardFeb 17, 2015

+190-59

Commits

Commits on Feb 17, 2015

• Do not require velvet

  

  Martin Hunt

  committed
  f088ae9

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• Use spades by default ; check dependencies

  

  Martin Hunt

  committed
  d3f030b

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• Add --spades_other option, remove --spades_only_assembler option

  

  Martin Hunt

  committed
  95e8d9a

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• Improve verbose output; use --trusted-contigs

  

  Martin Hunt

  committed
  0cee26e

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• Be verbose when required

  

  Martin Hunt

  committed
  b9bb4d4

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• Only check path/version for assembler being used

  

  Martin Hunt

  committed
  848494f

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• Tweak usage

  

  Martin Hunt

  committed
  a1dee8e

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• Do not check for spades

  

  Martin Hunt

  committed
  5e0c2c2

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• Require smalt version 0.7.4 or higher

  

  Martin Hunt

  committed
  1c436d5

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• Mummer, SPAdes dependency; tweak usage

  

  Martin Hunt

  committed
  3d0a3ba

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