Underlying tools
================

The ``microGWAS`` pipeline uses a number of computational tools
underneath, which you should try to cite in any publication that uses the results
produced by the pipeline.

..  tip::

    If you are the author of one the tools and spot an error in the
    references, please get in touch `by opening an issue on the
    repository <https://github.com/microbial-pangenomes-lab/gwas_template/issues>`__.

* ``unitig-counter``: `10.1371/journal.pgen.1007758 <https://doi.org/10.1371/journal.pgen.1007758>`__ and `10.1128/mbio.01344-20 <https://doi.org/10.1128/mbio.01344-20>`__
* ``mlst``: `Seemann T, mlst <https://github.com/tseemann/mlst>`__ and `10.12688/wellcomeopenres.14826.1 <https://wellcomeopenresearch.org/articles/3-124/v1>`__
* ``abritamr``: `10.1038/s41467-022-35713-4 <https://doi.org/10.1038/s41467-022-35713-4>`__
* ``mash``: `10.1186/s13059-016-0997-x <https://doi.org/10.1186/s13059-016-0997-x>`__
* ``ggCaller``: `10.1101/gr.277733.123 <https://doi.org/10.1101/gr.277733.123>`__
* ``panaroo``: `10.1186/s13059-020-02090-4 <https://doi.org/10.1186/s13059-020-02090-4>`__
* ``fasttree``: `10.1371/journal.pone.0009490 <https://doi.org/10.1371/journal.pone.0009490>`__
* ``snp-sites``: `10.1099/mgen.0.000056 <https://doi.org/10.1099/mgen.0.000056>`__
* ``snippy``: `Seemann T, snippy <https://github.com/tseemann/snippy>`__
* ``bcftools``: `10.1093/gigascience/giab008 <https://doi.org/10.1093/gigascience/giab008>`__
* ``limix``: `10.1101/003905 <https://doi.org/10.1101/003905>`__
* ``ALBI``: `10.1016/j.ajhg.2016.04.016  <https://doi.org/10.1016/j.ajhg.2016.04.016>`__
* ``sequence_unet``: `10.1186/s13059-023-02948-3 <https://doi.org/10.1186/s13059-023-02948-3>`__
* ``pyseer``: `10.1093/bioinformatics/bty539 <https://doi.org/10.1093/bioinformatics/bty539>`__ and `10.1101/852426 <https://doi.org/10.1101/852426>`__
* ``bwa``: `10.48550/arXiv.1303.3997 <https://arxiv.org/abs/1303.3997>`__
* ``bedtools``: `10.1093/bioinformatics/btq033 <https://doi.org/10.1093/bioinformatics/btq033>`__ and `10.1093/bioinformatics/btr539 <https://doi.org/10.1093/bioinformatics/btr539>`__
* ``eggnog-mapper``: `10.1093/molbev/msx148 <https://doi.org/10.1093/molbev/msx148>`__
* ``panfeed``: `10.1099/mgen.0.001129 <https://doi.org/10.1099/mgen.0.001129>`__