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Good things to do if time #3

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rmcolq opened this issue Dec 13, 2015 · 0 comments

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rmcolq commented Dec 13, 2015

Allow bam file (or sorted, or sorted indexed bam file) to be input and skip the relevant steps in cortex_polish.pl, where the bam is a map of the reads to the draft assembly
Allow a bam file to be input where the reads are mapped to a mysterious reference (as in our JR samples)
Sort out changes in default parameters if "ont" input
Make the cleanfile given threshold parameter for manual cleaning.

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