Quality trimming for denovo assembly

Question

[th526]

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

Answer 1

[Philipp Bayer]

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