I was wondering if still the data would be processed correctly, if I know that some read-pairs may be too short to overlap.
Let’s say I have a read pair:
read2: CCCAAA(...)CCCGGG (already reversed)
and I know they are too short to overlap and clearly
make.contigs will merge them incorrectly so to not lose this data I could “glue” them manually to create such contig:
and then I’d mix such contigs with the other “correct” contigs created by
Is it really idea to use the data like this?