Hi, So I am trying to build a variation graph from a set of short contigs produced by assembly tools. To elaborate about the problem, so I know there are quite a few ways in which you can construct a variation graph from a set of contigs produced by assembly tools like vg, poa, pgga, seqwish etc. I am dealing with viral quasispecies here. So, tools like SAVAGE, Haploclique produce shorter contigs, so I want to build a variation graph from these produced contigs. I tried it with vg but they update VG quite frequently so it doesn't seem to work for previous versions. I am looking for the best way available today to build a variation graph from the available methods. Do you guys have any suggestions for the same? Thank you.
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