reduce scaffolding params default values

dnanexus-archive / viral-ngs

viral-ngs

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reduce scaffolding params default values #43

Closed dpark01 closed 8 years ago

dpark01 commented 8 years ago

For scaffolding, our own default practice has been to significantly lower the min_length_fraction and min_unambig cutoffs to 0.5 for each. This just reduces the number of jobs that hit a PoorAssemblyError and allows for more partial genomes to come out the analysis.

tomkinsc commented 8 years ago

The relevant lines are here: https://github.com/dnanexus/viral-ngs/blob/dnanexus/viral-ngs-assembly-scaffolding/dxapp.json#L44-L54

dpark01 commented 8 years ago

Looks like I accidentally fixed this one already