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Option to use Spades and multithreading for Bowtie2 and Spades #210

Merged
merged 3 commits into from
Feb 2, 2018
Merged

Option to use Spades and multithreading for Bowtie2 and Spades #210

merged 3 commits into from
Feb 2, 2018

Commits on Feb 1, 2018

  1. Option to run subprocess w/o shell

    Andrey Tovchigrechko committed Feb 1, 2018
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  2. Remove reference to spades options in tests that are not using spades. 

    Cleanup tmp dirs before copytree in case the test harness is repeated
in a directory after previous run has failed with unhandled exceptions.
    Andrey Tovchigrechko committed Feb 1, 2018
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  3. Reintroduce Spades as another assembly option. Multithreading for Spa… 

    …des and Bowtie2.

Spades improves upon default fermilight on challenging datasets with highly uneven coverage
(viral, amplicon, single-cell).
Multithreading for Spades and Bowtie2 subprocesses is adaptive - kicks in at the end of
a multiprocessing map run when idle threads were appearing otherwise (or in cases of overall
fewer clusters than total threads).
    Andrey Tovchigrechko committed Feb 1, 2018
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