using 250bp paired reads in pilon (which the reads of a pair may overlap each other)

broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool

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using 250bp paired reads in pilon (which the reads of a pair may overlap each other) #60

Closed dgordon562 closed 5 years ago

dgordon562 commented 6 years ago

Would Pilon have any problem with 250bp paired reads in which the reads overlap each other?

melop commented 6 years ago

I don't see what would be a problem specific to 250x2PE libraries, because some reads will overlap even in 100x2 PE libraries. I have applied pilon using 250x2PE libraries without seeing an error.