Request optimized default alignment parameters for ONT data

[seboyden]

The default settings for --alignment-params are optimized for PacBio HiFi reads. You suggest increasing the gap-open values f and g for ONT reads with a higher indel error rate, but it's not clear what appropriate values would be. Would be great to have a set of optimized ONT default values.

[heliziii]

Hello. Thank you for using LongTR. I tested with values -1 for f and g instead of -10 and alignments seemed more accurate, but we did not systematically test different values. Please let me know if you have any other questions.

Best,
Helia