Edit: I should have refreshed before posting, Maubp's suggestion is probably easier!
You might be able to just use grep (grep -v -f ids.file ...), though you might have to collapse the read name and sequence onto one line (with awk) first, then pipe that into grep and pipe the output back to awk to split things back again.
You might be able to just use grep (grep -v -f ids.file ...), though you might have to collapse the read name and sequence onto one line (with awk) first, then pipe that into grep and pipe the output back to awk to split things back again.
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