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Old 04-10-2017, 03:45 AM   #2
Location: Sweden

Join Date: Aug 2011
Posts: 30

Discovar de novo was designed specifically for 2x250 bp reads so you could give it a try. Of course it is recommended to have inserts longer than the sequencing reads (500 bp in your case) but it goes for all assemblers and doesn't mean your assembly is not valid. Best way to improve the assembly would likely be to add long/linked reads though.
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