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Old 04-10-2017, 09:47 AM   #4
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Originally Posted by Vinn View Post
I have got data generated from 2x250 bp with 350 bp insert for fungal genome assembly. I got very good results from SPAdes, but later discovered that SPAdes recommends an insert of 550-700 bp for 2x250 bp sequencing.
I think that means "If you want to use SPAdes for 2x250bp reads, we recommend you target you libraries for 550-700bp" rather than "If you have a library outside of 550-700bp, don't use SPAdes". Once you have the library, it's too late, but SPAdes is very flexible with insert sizes.

As Genomax mentioned, you might try merging the reads first; I have found that to improve SPAdes assemblies.
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