I recently wanted to see how a bunch of contigs align to a telomere to telomere genome assembly so I used minimap2 to align them and now I have 2 alignment files, one as a.paf file and one as a .sam file. I'm wondering if there is an easy way to visualize the alignments where you just provide the fasta file with the genome assembly and one of the alignment files (or with the fasta file for the t2t assembly, the fasta file for the contigs, and one of the alignment files)
It doens't even have to conserve sequence data. Just need to have a general idea of where the reads are mapping. So for example if I could get a visualization that contigs 2, 4, and 8 map to bases regions 100-12000, 13000-40000, and 45000-65000 of chromosome 1, but i don't have any of the sequence alignment data then that's totally fine.
Is there an easy way to do this (ideally in R)
Why not use IGV with SAM file?
If you want a text based viewer then ASCIIGenome: https://asciigenome.readthedocs.io/en/latest/
Tablet https://ics.hutton.ac.uk/tablet/ is more of an assembly viewer, but useful as very fast for very deep data.