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Old 01-12-2017, 09:21 AM   #1
anth
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Location: USA

Join Date: Jul 2011
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Default Optimal insert size for de novo assembly from PE150 reads

In the past, I have had reasonable success with de novo assembly of non-model eukaryotes with insert sizes of ~300 bp, using 100 bp PE and Trinity for assembly.

With 150 bp PE reads and the current version of Trinity, is a mean insert size of ~300 bp still generally optimal, or would a longer mean insert size likely benefit the assembly?

(RNA will be poly-a selected, with libraries constructed using the NEBNext® Ultra™ Directional kit.)

Thanks in advance!
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