In the "get_input_files" function in SeqSero2_package.py, both forward and reversed reads are returned for option '2'(pair-end reads, seperated). However, in that same file, on line 1469, we see that only forward reads are being used:
"input_file = for_fq #-k will just use forward because not all reads were used"
Why are all reversed reads ignored for that type of input? Doesn't this reduce the sensitivity and accuracy of this method? Why wasn't this mentioned in the article?
In the "get_input_files" function in SeqSero2_package.py, both forward and reversed reads are returned for option '2'(pair-end reads, seperated). However, in that same file, on line 1469, we see that only forward reads are being used:
"input_file = for_fq #-k will just use forward because not all reads were used"
Why are all reversed reads ignored for that type of input? Doesn't this reduce the sensitivity and accuracy of this method? Why wasn't this mentioned in the article?