What is a proper "-min_read_len" options? about nextpolish HOT 2 CLOSED

If you use lgs_options = -min_read_len 10k -max_read_len 150k -max_depth 60, which means you will set -min_read_len to 10k, if you use lgs_options = -max_read_len 150k -max_depth 60, which means you do not set -min_read_len, so the -min_read_len is 1k (default value).

min_read_len does not make a big difference in polishing your genome if you have enough data, but if you only have <60x data, just set it to 1k, in order to use more data for polishing.

from nextpolish.

If you use lgs_options = -min_read_len 10k -max_read_len 150k -max_depth 60, which means you will set -min_read_len to 10k, if you use lgs_options = -max_read_len 150k -max_depth 60, which means you do not set -min_read_len, so the -min_read_len is 1k (default value).

min_read_len does not make a big difference in polishing your genome if you have enough data, but if you only have <60x data, just set it to 1k, in order to use more data for polishing.

Thank you ,sir
Have a nice day

from nextpolish.