I'm pretty new to the stuff and after reading some papers and posts I'm still not sure what I should do so maybe somebody with more experience could shed some light.
After I got my contings with Canu I would liike to use Pilon and polish them with Illumina reads. After trimming and quality control they are 20-301 in length. In Pilon docs they wrote about using BWA MEM but then there's minimap2 which is faster (kinda important for me) but then again not so good with short-reads. What would you recommend? What about filtering those reads for 100-301 in length (that would be around 95% of all reads I think) and then going with minimap2? Would appreciate any information :D