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Old 04-14-2017, 05:01 PM   #4
luc
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Location: US

Join Date: Dec 2010
Posts: 343
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Trinity is the standard for de novo transcriptome assemblies. Thus also the artifacts it produces are relatively wellk nown.
Sorry, I have never used CLC for this purpose. I would suggest to contact CLC for suggested settings for transcriptomes (I can't imagine the defaults are optimal).
For genome assemblies CLC has the advantage that it will work with all kinds of data (all kinds of read lengths, paired or not paired, and even low quality data). In short it is extremely robust for this purpose.
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