23 months ago by
The tool Select can pattern match, one pattern at a time, through a regular expression. But that won't be the best solution for this query.
Instead, try a mapping tool such as Lastz. Create a custom reference genome of the 100 query sequences, map the fastq dataset, then filter the output by percent identity and coverage.
I cannot help you with BBDUK, but perhaps someone else here can, or you can review other online sites (a google brings up much usage discussion).
Thanks, Jen, Galaxy team