vg
vg copied to clipboard
vgteam
how to construct a graph of two genomes from two species
Hello,Professor I have two genomes from two species. My end goal is to construct a graph of the two genomes from two species and then map tens of illumina short reads to the graph. But I am not sure how to construct the graph taking a VCF file and the reference sequence by "vg construct". Should I combine the two genomes from two species into a input fasta by "cat" ? Also, how do I generate the prior vcf needed by "vg construct"? I would appreciate it if you could give me any suggestions. Best wishes !
You should take a look at the PGGB pipeline, which builds a graph by aligning the input sequences. vg construct is primarily intended for building a graph from a reference sequence and a set of variants in a VCF file.
Hello,Professor
I have read the PGGB pipline you recommended. I still have some confusion with vg. The reference sequence is a genome assembly? In vg pipeline, How should I generate the vcf file of a set of variants. Maybe it is called through illumina reads of some samples of different species basing on the reference sequnece?
Looking forward with your reply!
Best wishes!
If you have an assembled reference sequence and a VCF file describing variation relative to the reference sequence, you use vg construct for building the graph. If you don't have a VCF file, you don't need it. If you have multiple assembled genomes, you should use other tools such as PGGB for building the graph.
Dear @jltsiren , after building the graph with PGGB with multiple genome can I use VG to call variants?
Yes. And there is even a command line option in pggb to run the variant deconstruction with VG.
On Tue, Feb 1, 2022, 01:58 Diego Mauricio Riaño-Pachón < @.***> wrote:
Dear @jltsiren https://github.com/jltsiren , after building the graph with PGGB with multiple genome can I use VG to call variants?
— Reply to this email directly, view it on GitHub https://github.com/vgteam/vg/issues/3508#issuecomment-1026367783, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABDQEJOAOYQVANZ7RNTBT3UY4V47ANCNFSM5K3L6PAA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
You are receiving this because you are subscribed to this thread.Message ID: @.***>
