ITS amplicons can have a great variation in length. Therefore the insert size may become too small to have a partial overlap. Better yet, the insert size may be long enough for a partial overlap, but then after trimming the prefixes from both reads you may run into a situation that requires complete overlap analysis instead of partial overlap.
Here is an example. Say this is read 1 in one of your ITS paired-end sequences:
To solve this issue a new parameter is required. When m/o (mismatches at the overlapped region) fails miserably, the algorithm should check "the other way around" alternative, and pick the one with the best m/o.
ITS amplicons can have a great variation in length. Therefore the insert size may become too small to have a partial overlap. Better yet, the insert size may be long enough for a partial overlap, but then after trimming the prefixes from both reads you may run into a situation that requires complete overlap analysis instead of partial overlap.
Here is an example. Say this is read 1 in one of your ITS paired-end sequences:
and this is read 2:
and this is your config.ini file to merge them:
And if you run these like this:
merge-illumina-pairs short.ini
read 1 and 2 will not merge. Because, after trimming prefixes, they will want to be aligned like this after the reverse-complementing read 2:
unlike our expected partial overlap situation:
To solve this issue a new parameter is required. When m/o (mismatches at the overlapped region) fails miserably, the algorithm should check "the other way around" alternative, and pick the one with the best m/o.