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A standalone package for using deep mutational scanning data to predict the phenotypes of untested sequences from a multiple-sequence alignment.

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matsengrp/dmsa-pred

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dmsa-pred

A standalone package for predicting variant phenotypes given a multiple sequence alignment and DMS data.

If this is used as a submodule to a nextflow build, use we reccomend following this guide as a workflow

When intergrating into an existing Nextstrain build, the primary steps to take are:

  1. Add this as a submodule
  2. Add the appropriate dependency of the resulting JSON's into the main workflow
  3. install the dependencies:
$ conda activate ~/.nextstrain/runtimes/conda/env
$ snakemake --use-conda --cores 2 --create-envs-only --configfile dmsa-pipeline/dmsa-pred-reference.yaml

Now you can run the pipeline:

snakemake --use-conda --cores 4 --configfile dmsa-pipeline/dmsa-pred-reference.yaml

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A standalone package for using deep mutational scanning data to predict the phenotypes of untested sequences from a multiple-sequence alignment.

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