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Spades try all kmers #40

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merged 3 commits into from
Oct 13, 2015

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martinghunt
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Previously, Circlator ran SPAdes with a list of kmers, longest first. Circlator would stop at the first assembly that was successful (ie error code==0). This PR changes the default behaviour to try all kmers, and choose the assembly with the best N50 (this is not always the one with the biggest kmer). Also added an option to use the old behaviour.

aslett1 added a commit that referenced this pull request Oct 13, 2015
@aslett1 aslett1 merged commit 200e8fa into sanger-pathogens:master Oct 13, 2015
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