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Pangenome graphs (review article on graph-based pangenomic methods)
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Cut mapper refs #84

Closed jeizenga closed 4 years ago

jeizenga commented 4 years ago

I cut the error correction section on account of it not really being a pangenomic method per se (or at least not necessarily). That brought us down quite a few refs. I also removed the de Bruijn graph mappers, with the exception of GraphAligner, and I emphasized GraphAligner's mapping to general graphs rather than to de Bruijn graphs. I also started switching over to \textsc for tool names.

Let me know if anyone strongly disagrees with these changes.

ekg commented 4 years ago

I was hoping to add a small amount to the error correction section (or refer to it in the discussion) as an unexplored technique for pangenome construction. I also thought that the coverage of mapping tools was good. I was hoping to cut down on references to basic biology that are included just for completeness and not as part of the material we are reviewing. Will take a look at what you've done. The last thing I'd like to skimp on is graph alignment and mapping.

On Fri, Nov 22, 2019, 00:57 Jordan Eizenga notifications@github.com wrote:

I cut the error correction section on account of it not really being a pangenomic method per se (or at least not necessarily). That brought us down quite a few refs. I also removed the de Bruijn graph mappers, with the exception of GraphAligner, and I emphasized GraphAligner's mapping to general graphs rather than to de Bruijn graphs. I also started switching over to \textsc for tool names.

Let me know if anyone strongly disagrees with these changes.

You can view, comment on, or merge this pull request online at:

https://github.com/vgteam/graph-genomics-review/pull/84 Commit Summary

  • remove de bruijn mappers and error correction
  • switch tools to textsc in relating and applicatinos
  • trim a little from transcript mapping and variant calling intro
  • trim some fat

File Changes

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