pyseer --phenotypes phenotypes.tsv --kmers kmers.gz --distances structure.tsv --min-af 0.01 --max-af 0.99 --cpu 15 --filter-pvalue 1E-8
Kmers-based GWAS analysis is particularly well suited for bacterial samples, given their high genetic variability. This approach has been implemented by Lees, Vehkala et al., in the form of the SEER software.
The reimplementation presented here should be consistent with the current version of the C++ seer (though we do not guarantee this for all possible cases).
Lees, John A., Galardini, M., et al. "pyseer: a comprehensive tool for microbial pangenome-wide association studies". Bioinformatics 34:4310–4312 (2018).
Lees, John A., et al. "Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes." Nature communications 7:12797 (2016).
Full documentation is available at readthedocs.
You can also build the docs locally (requires
sphinx) by typing:
cd docs/ make html
Between parenthesis the versions the script was tested against:
If you would like to use the
scree_plot_pyseer script you will also need to have
If you would like to use the scripts to map and annotate kmers, you will also need
The easiest way to install pyseer and its dependencies is through
conda install pyseer
If you need
conda, download miniconda
and add the necessary channels::
conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge
pyseer can also be installed through
python -m pip install pyseer
If you want multithreading make sure that you are using a version 3 python interpreter::
python3 -m pip install pyseer
If you want the next pre-release, just clone/download this repository and run:
Copyright 2017 EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.