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viral-ngs
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s/novoalign_options/aligner_options/g #62

Closed tomkinsc closed 7 years ago

tomkinsc commented 7 years ago

Addresses https://github.com/dnanexus/viral-ngs/issues/60

mlin commented 7 years ago

@tomkinsc incorporating -- it looks like the intended options are much more stringent than the unintended defaults that were being used, in that many fewer reads (roughly half) come out mapped to the final assembly -- just double-checking is this expected? https://github.com/dnanexus/viral-ngs/commit/21c8d00d6d0cf8860a901306485502df15902712

tomkinsc commented 7 years ago

That's expected! We caught the discrepancy due to seeing many more reads than our local pipeline.