Question: Quality trimming for denovo assembly
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gravatar for th526
23 months ago by
th5260
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 • 1.1k views
ADD COMMENTlink modified 23 months ago by Philipp Bayer6.4k • written 23 months ago by th5260
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gravatar for Philipp Bayer
23 months ago by
Philipp Bayer6.4k
Australia/Perth/UWA
Philipp Bayer6.4k 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: https://github.com/tseemann/shovill

ADD COMMENTlink written 23 months ago by Philipp Bayer6.4k
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