Question: Quality trimming for denovo assembly
gravatar for th526
12 months ago by
th5260 wrote:

Is quality trimming of raw reads (Illumina Paired End; 2 X 300 bp) for de novo assembly using SPAdes is recommended? Any suggestions ? I have Q score >30 up to 250th base in Forward reads and Q score drops below 25 from base position 180 in reverse reads. Is it advisable to do quality trimming in these case?

Regards Thippesh

assembly • 517 views
ADD COMMENTlink modified 12 months ago by Philipp Bayer5.7k • written 12 months ago by th5260
gravatar for Philipp Bayer
12 months ago by
Philipp Bayer5.7k
Philipp Bayer5.7k wrote:

SPAdes runs its own read data trimming and error correction so you don't have to do that.

However it's still highly advisable to run adapter trimming, for example using Trimmomatic. Torsten Seeman also has a pipeline around SPAdes called shovill which has a --trim option which will run Trimmomatic for you:

ADD COMMENTlink written 12 months ago by Philipp Bayer5.7k
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