Question about extracted.filtered.fa

[HuangLoong]

Hello, I have a question about the ’extracted.filtered.fa‘ file in the output of stage_two . May I ask if the file contains complete ARG-carrying read or only a partial sequence (sequence cutoff) hit in the database? If I want to obtain all ARG-carrying reads, is this file my target?

[xinehc]

they are all ARG-carrying reads that pass stage-two's cutoffs