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Nextomics / NextPolish

Fast and accurately polish the genome generated by long reads.
GNU General Public License v3.0
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What is a proper "-min_read_len" options? #45

Closed AntetokounmJie closed 4 years ago

AntetokounmJie commented 4 years ago

Hi sir, sorry to bother you again.

I use nextDenovo to assembly my genome, and the recommanded seed_cutoff is about 30k generated by seq_stat with "-d 45". And a i got pretty good assembly result with long N50. Then i wanna use nextpolish to polish my draft genome with my ONT and Illumina reads. When i started to set to config of nextpolish, a little confusion came out. I see the "-min_read_len" in here is 10k but the default is 1k. So how can i set a proper one, or maybe i should use seq_stat to get a "-min_read_len" due to the "-max_depth" of lgs_options?

Thanks a lot :)

moold commented 4 years ago

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.

AntetokounmJie commented 4 years ago

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