The objective of my study is to try and correct a pool of nanopore reads and then filter out any low quality reads that didn't get corrected (below for an example of what I mean. There are 2 highly erroneous reads in this snippet that stand out that I want filtered out of this dataset)
I'm thinking of using minimap2, but I don't know what parameters to set or how to even go about picking good parameters for this? I'm worried that the -x ava-ont preset won't work well, because most of the reads are not standard nanopore reads, but rather high-quality corrected reads. If anyone has any ideas or recommendations for how to best go about doing the alignment or an even better way to filter out these low quality reads without the use of a reference genome please let me know. I can't just filter them out based on thread scores because the corrections result in .fasta files, not .fastq.
