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-   -   Optimal insert size for de novo assembly from PE150 reads (http://seqanswers.com/forums/showthread.php?t=73572)

anth 01-12-2017 09:21 AM

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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