search

Nextomics / NextPolish2

Repeat-aware polishing genomes assembled using HiFi long reads
Other
63 stars 3 forks source link

Process file containing polish sites and sequences #12

Closed justdx closed 9 months ago

justdx commented 9 months ago

I used nextPolish2 to improve my Arabidopsis assembly, and I generated the polished file smoothly. But the end result seems to be only one Fasta file, I would like to ask if it is possible to get a file with polished location and sequence, like Pilon's change.txt? In addition to this, I would like to ask if you have any suggestions regarding the kmer size to use? Is it just that the more k the better?

moold commented 9 months ago
  1. No
  2. You can try 2 Kmers or 3 kmers (when inputting more than 3 kmers, the results will not be greatly improved), such as K=21 & 31, K=31 &41, K=31,41,51... and find the best result. The optimal kmer set depends on your input.