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tools for working with genome variation graphs
https://biostars.org/tag/vg/
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Aligning PacBio reads to assembly graph? #608

Open shilpagarg opened 7 years ago

shilpagarg commented 7 years ago

Hi, anyone is interested in aligning PacBio reads to assembly graph? I tried few examples, it looks vg does not do the right thing. Here are the listed things:

  1. align pacbio reads to assembly (base) graph and output sorted alignments in the nodeID space of base graph.
  2. augment the base graph with pacbio alignments and output sorted pacbio alignments in nodeID space of augmented graph. It is good to output augmented graph as well.
edawson commented 7 years ago

Hey Shilpa,

I'd be interested in trying this, especially since it's a lot like the stuff I'm working on with HPV. Are you just using the yeast data?

Where does vg choke in the above pipeline?

shilpagarg commented 7 years ago

That's great, I write you an email to point you to the dataset. I would mention the steps as well. Is it OK?

On Jan 4, 2017 18:36, "Eric T. Dawson" notifications@github.com wrote:

Hey Shilpa,

I'd be interested in trying this, especially since it's a lot like the stuff I'm working on with HPV. Are you just using the yeast data?

Where does vg choke in the above pipeline?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/vgteam/vg/issues/608#issuecomment-270433653, or mute the thread https://github.com/notifications/unsubscribe-auth/AHEq5xuwVD7rY3-RV8HO_noZ2VXGAD84ks5rO9iXgaJpZM4LZw3E .

ekg commented 7 years ago

We should use this thread to figure out and document the best pattern for aligning pacbio and nanopore reads with vg.

On Wed, Jan 4, 2017, 8:22 PM shilpagarg notifications@github.com wrote:

That's great, I write you an email to point you to the dataset. I would mention the steps as well. Is it OK?

On Jan 4, 2017 18:36, "Eric T. Dawson" notifications@github.com wrote:

Hey Shilpa,

I'd be interested in trying this, especially since it's a lot like the stuff I'm working on with HPV. Are you just using the yeast data?

Where does vg choke in the above pipeline?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/vgteam/vg/issues/608#issuecomment-270433653, or mute the thread < https://github.com/notifications/unsubscribe-auth/AHEq5xuwVD7rY3-RV8HO_noZ2VXGAD84ks5rO9iXgaJpZM4LZw3E

.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/vgteam/vg/issues/608#issuecomment-270461553, or mute the thread https://github.com/notifications/unsubscribe-auth/AAI4ER2MdSARoaZMmCllwW0yjrJ_xL4wks5rO_F5gaJpZM4LZw3E .

ekg commented 7 years ago

Could we work up a test example to show that ideas we have make sense?

shilpagarg commented 7 years ago

Sure, the test assembly graph at Sanger farm: erik/final_exp/two_snvs_assembly.gfa. or do u want to create o extent this once and later simulate some reads?

ekg commented 7 years ago

Could we upload a small example to github? If it's small enough we can include it in the tests.

Do you have an example fragment which you think is representative that we could work from?