If I'm not wrong with the command subseq of seqtk program I am able to fish out some reads with a specific sequence, is that right?
the cmd is:
seqtk subseq in.fastq list.txt > out.fastq
In this case it is not clear the structure of the file list.txt, are the sequence I want to look for enough? I didn't find anything about this file in the documents of the seqtk.