Gap closing in repetitive regions can cause problems
Closed this issue · 2 comments
Dmitry-Antipov commented
ONT reads from repetitive regions may align to any tip in that region, and thus, cause excessive connections during gap closing.
See utig1-9680 & utig1-18185 on gorilla run
Plan is to check whether the found gap is near tangle, and do not close at least tip-notip gaps in that cases.
skoren commented
Has this been addressed with our gap filling changes in v2.0?
Dmitry-Antipov commented
Yup, I think this was completely fixed