To align long and almost identical sequences - pb-cdunn/blasr GitHub Wiki

In order to align very long and almost identical sequences (e.g., assembled sequences to reference), you may try the following options:

• -minMatch 15: almost identical sequences allow longer seeds

• -maxMatch 20: always set a maxMatch regardless

• -advanceHalf: a trick for speeding up alignments at the cost of sensitivity.

• -advanceExactMatches 10: a trick for speeding up alignments with (match - E) fewer anchors. Use this to align assembled sequences to reference.

• -fastMaxInterval: search for maximal increasing intervals as alignment candidates using a fast but not as exhaustive way.

• -fastSDP: use a fast heuristic algorithm to speed up sparse dynamic programming

• -aggressiveIntervalCut: agressively filter out non-promising alignment candidates if there exists at least one promising candidate. When this is turned on, blasr is likely to ignore short alignments of ALU elements.