DiscoSNP++ pre-processing fastq files

Question

[tkitapci]

Hi,

Is there any "best practice recommendations" for pre-processing fastq files prior to use DiscoSNP? Should I run Trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic) or a similar tool?

Anybody knows the effect of quality trimming the reads on the outcome? (Did anybody run a benchmark running DiscoSNP on raw reads and quality trimmed reads and compared the results?)

Thanks

Best Regards
Hamdi

Answer 1

[pierre.peterlongo]

Hi again,

We don't have this kind of feedback using or not preprocessed reads.

In theory discoSnp++ (from 2.2.0) automatically detects the good thresholds for selecting non erroneous k-mers. However, results with or without preprocessing would be really valuable.

Pierre

[tkitapci]

Hi Pierre,

I have run discoSNP++ on my raw fastq files. I am planning to do read trimming and error correction and run it again. I can post my results here later.

Thanks

Best Regards

T. Hamdi Kitapci