Question: Best practice for de novo assembly
gravatar for codsorre
8 months ago by
codsorre10 wrote:

Hello all, I am new to de novo assembly and working with sequencing data in general. I am working with some paired end sequences. I just ran them through trimmomatic to remove adapters and am left with the forward and reverse paired sequences, and the forward and reverse unpaired sequences. When running trinity for de novo assembly, would it be the best practice to just assembly using the paired sequences for all samples I am analyzing, or should I include the unpaired sequences as well? What would be the pros or cons of each?


assembly • 239 views
ADD COMMENTlink modified 8 months ago by Michael Dondrup48k • written 8 months ago by codsorre10
gravatar for Michael Dondrup
8 months ago by
Bergen, Norway
Michael Dondrup48k wrote:

Trinity has a switch to run trimmomatic inside its pipeline. However, if you ran it already, I don't see much of a problem in using the unpaired sequences as well. Do you see many unpaired fragments, I normally see only a tiny fraction. If there are too many that might indicate a problem with the library. Stil, unpaired fragments will provide coverage and kmer information for building the De Bruijn graph. If in a later step paired reads are required for orienting contigs, the unpaired will be disregarded.

ADD COMMENTlink written 8 months ago by Michael Dondrup48k

That makes sense, thanks. Relatively speaking, how many unpaired fragments is too many? Roughly about 5% seem to be going to unpaired

ADD REPLYlink written 8 months ago by codsorre10
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