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Forum: Bioinformatics 09-15-2017, 05:30 AM
Replies: 347
Views: 184,309
Posted By cuencam
Hi EssigSchurke The flag is minlength=10 ...

Hi EssigSchurke
The flag is minlength=10

The whole command is
bbduk.sh in=input.fq out=output.fq minlength=10

Edit:

I misread your question. The command provided by jazz710 is the...
Forum: Bioinformatics 09-13-2017, 03:19 AM
Replies: 347
Views: 184,309
Posted By cuencam
Thanks for this response! I'm pretty sure that...

Thanks for this response! I'm pretty sure that your excellent user support is only comparable to the high quality of your tools!

I will implement quality-trimming at a higher threshold and then...
Forum: Bioinformatics 09-12-2017, 05:50 AM
Replies: 347
Views: 184,309
Posted By cuencam
Hi Brian, In the same lines of my previous...

Hi Brian,
In the same lines of my previous question, what is the rationale of using maq=10? We are interesting in de novo assembly of metagenomic data and we were worried that low quality bases at...
Forum: Bioinformatics 08-15-2017, 12:29 AM
Replies: 347
Views: 184,309
Posted By cuencam
Hi Brian, Thanks for such a quick response, and...

Hi Brian,
Thanks for such a quick response, and implementing this so fast!
Our interest is that during SNV calling in low coverage regions or low abundance taxa (in metagenomics) base quality can...
Forum: Bioinformatics 08-11-2017, 03:34 AM
Replies: 347
Views: 184,309
Posted By cuencam
Hi Brian, I would like to switch from solexaqa...

Hi Brian,
I would like to switch from solexaqa to BBduk for my read trim and filtering option, however since we are working with bacterial strains typification we would like to have the option to...
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