# :icon-zap: Software used in Harpy
Harpy is the sum of its parts, and out of tremendous respect for the developers involved in the included software, we would like to highlight the tools directly involved in Harpy's many moving pieces.
If any tools were missed, please let us know!

Issues with specific tools might warrant a discussion with the authors/developers on the repositories of these projects.

## Standalone Software
{.compact .clean}
| Software           | Links                                                                                                                                                                                                                    |
| :----------------- | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| arcs               | [github](https://github.com/bcgsc/arcs), [publication](https://doi.org/10.1101/100750)                                                                                                                                   |
| athena             | [github](https://github.com/abishara/athena_meta), [publication](https://doi.org/10.1038/nbt.4266)                                                                                                                       |
| bash               | [website](https://www.gnu.org/software/bash/)                                                                                                                                                                            |
| bcftools           | [github](https://github.com/samtools/bcftools), [website](https://samtools.github.io/bcftools/bcftools.html)                                                                                                             |
| conda              | [github](https://github.com/conda)                                                                                                                                                                                       |
| dmox               | [gitlab](https://gitlab.mbb.cnrs.fr/ibonnici/dmox)                                                                                                                                                                       |
| fastp              | [github](https://github.com/OpenGene/fastp), [publication](https://doi.org/10.1093/bioinformatics/bty560)                                                                                                                |
| HapCUT2            | [github](https://github.com/vibansal/HapCUT2) ,[publication](https://doi.org/10.1101/gr.213462.116)                                                                                                                      |
| htslib             | [website](http://www.htslib.org/)                                                                                                                                                                                        |
| JupyterBook        | [github](https://github.com/jupyter-book/jupyter-book), [MyST](https://github.com/jupyter-book/mystmd)                                                                                                                   |
| LEVIATHAN          | [github](https://github.com/morispi/LEVIATHAN) ,[publication](https://doi.org/10.1101/2021.03.25.437002)                                                                                                                 |
| links              | [github](https://github.com/bcgsc/links), [publication](https://gigascience.biomedcentral.com/articles/10.1186/s13742-015-0076-3)                                                                                        |
| LRez               | [github](https://github.com/morispi/LRez), [publication](https://academic.oup.com/bioinformaticsadvances/article/1/1/vbab022/6375438?login=false)                                                                        |
| minibwa            | [github](https://github.com/lh3/minibwa), [preprint](https://arxiv.org/abs/2606.15357)                                                                                                                                   |
| minimap2           | [github](https://github.com/lh3/minimap2), [publication](https://doi.org/10.1093/bioinformatics/bty191)                                                                                                                  |
| NAIBR              | [github](https://github.com/raphael-group/NAIBR), [github (fork)](https://github.com/pontushojer/NAIBR) ,[publication](https://doi.org/10.1093/bioinformatics/btx712)                                                    |
| papermill          | [github](https://github.com/nteract/papermill)                                                                                                                                                                           |
| python             | [website](https://www.python.org/)                                                                                                                                                                                       |
| QuickDeconvolution | [github](https://github.com/RolandFaure/QuickDeconvolution), [publication](https://doi.org/10.1093/bioadv/vbac068)                                                                                                       |
| samtools           | [github](https://github.com/samtools/samtools), [website](http://www.htslib.org/), [publication](https://doi.org/10.1093/gigascience/giab008)                                                                            |
| seqtk              | [github](https://github.com/lh3/seqtk)                                                                                                                                                                                   |
| Snakemake          | [github](https://github.com/snakemake/snakemake), [publication](https://f1000research.com/articles/10-33/v1)                                                                                                             |
| spades             | [spades](http://ablab.github.io/spades/), [cloudspades](https://github.com/ablab/spades/tree/cloudspades-ismb), [spades](https://doi.org/10.1002/cpbi.102), [cloudspades](https://doi.org/10.1093/bioinformatics/btz349) |
| STITCH             | [github](https://github.com/rwdavies/STITCH), [publication](https://doi.org/10.1038%2Fng.3594)                                                                                                                           |
| strobealign        | [github](https://github.com/ksahlin/strobealign), [publication](https://doi.org/10.1186/s13059-022-02831-7)                                                                                                              |
| tigmint            | [github](https://github.com/bcgsc/tigmint), [publication](https://doi.org/10.1186/s12859-018-2425-6)                                                                                                                     |
| whatshap           | [github](https://github.com/whatshap/whatshap), [publication](https://doi.org/10.1101/085050)                                                                                                                            |

## Software Packages
{.compact .clean}
| Package    |     Language      | Links                                                                                                 |
| :--------- | :---------------: | :---------------------------------------------------------------------------------------------------- |
| AG-Grid    |    JavaScript     | [github](https://github.com/ag-grid/ag-grid)                                                          |
| altair     | Python/JavaScript | [github](https://github.com/vega/altair)                                                              |
| click      |      Python       | [github](https://github.com/pallets/click)                                                            |
| IPython    |      Python       | [github](https://github.com/ipython/ipython)                                                          |
| numpy      |      Python       | [github](https://github.com/numpy/numpy)                                                              |
| pandas     |      Python       | [github](https://github.com/pandas-dev/pandas)                                                        |
| polars     |    Python/Rust    | [github](https://github.com/pola-rs/polars)                                                           |
| pysam      |      Python       | [github](https://github.com/pysam-developers/pysam)                                                   |
| rich       |      Python       | [github](https://github.com/Textualize/rich)                                                          |
| rich-click |      Python       | [github](https://github.com/ewels/rich-click)                                                         |
| vega-lite  |    JavaScript     | [github](https://github.com/vega/vega-lite), [publication](https://doi.org/10.1109/tvcg.2016.2599030) |