MAF to graph?

[dbrami]

Hi all, What's the easiest way for me to go from a existing multiple sequence alignment FASTA to a graph, for analysis in VG?

[ekg]

vg construct should have a facility to do this.

Two POA-based MSA algorithms, spoa and abPOA, can directly produce GFA. That could help.

[dbrami]

This is breakthrough insight for me! Now I just need to get VG to compile on my mac for proper toying around before running jobs on AWS...

On Tue, Feb 2, 2021 at 4:59 PM Erik Garrison notifications@github.com wrote:

vg construct should have a facility to do this.

Two POA-based MSA algorithms, spoa and abPOA, can directly produce GFA. That could help.

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[subwaystation]

Or you can make a conda environment and install vg in there: https://bioconda.github.io/recipes/vg/README.html.

[dbrami]

Hi Simon, Thank you so much for your response! I got so excited and kicked myself for not trying that! Alas, i'm still not having any luck:

(base) ➜ graphGenomes conda install -c bioconda vg

Collecting package metadata (current_repodata.json): done

Solving environment: failed with initial frozen solve. Retrying with flexible solve.

Collecting package metadata (repodata.json): done

Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

• vg Any suggestions? Otherwise, I will have to resort to Docker :/

On Tue, Feb 2, 2021 at 5:27 PM Simon Heumos notifications@github.com wrote:

Or you can make a conda environment and install vg in there: https://bioconda.github.io/recipes/vg/README.html.

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[subwaystation]

The following works for me:

conda create --name vg
conda activate vg
conda install -c bioconda vg

Typing vg I get:

vg: variation graph tool, version v1.30.0 "Carentino"

usage: vg <command> [options]

main mapping and calling pipeline:
  -- construct     graph construction
  -- index         index graphs or alignments for random access or mapping
  -- map           MEM-based read alignment
  -- giraffe       fast haplotype-aware short read alignment
  -- augment       augment a graph from an alignment
  -- pack          convert alignments to a compact coverage index
  -- call          call or genotype VCF variants
  -- help          show all subcommands

For more commands, type `vg help`.
For technical support, please visit: https://www.biostars.org/t/vg/

I suspect there is a conflict with your current environment and what vg requires.