Short read alignment to pangenome

Question

[arash.iranzadeh1980]

Hi,

I have a pangenome graph in dot format. I want to align short reads (fastq) to this graph. I tested vg but I got error (core dumped), any other tool for mapping reads to graph?

[h.mon]

Should you be aligning to .dot?

DOT is a standard format used by graphtools, a package for graph visualization designed by AT&T labs a long, long time ago. It's kind of human readable, but it's best used as an intermediate between vg and a PDF or SVG file.

You should probably align against the .gcsa index.