Best way to visualize .paf or .sam alignment to a fasta file
Entering edit mode
9 weeks ago
Mark • 0

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)

visualization sam fasta paf alignment • 346 views
Entering edit mode

Why not use IGV with SAM file?

If you want a text based viewer then ASCIIGenome:

Entering edit mode

Tablet is more of an assembly viewer, but useful as very fast for very deep data.


Login before adding your answer.

Traffic: 1950 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6