# :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}
| Software           | Links                                                                                                                       | Publication                                                                                                                                                                     |
|:-------------------|:----------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| ARCS suite         | [tigmint](https://github.com/bcgsc/tigmint), [arcs](https://github.com/bcgsc/arcs), [links](https://github.com/bcgsc/links) | [tigmint](https://doi.org/10.1186/s12859-018-2425-6), [arcs](https://doi.org/10.1101/100750), [links](https://gigascience.biomedcentral.com/articles/10.1186/s13742-015-0076-3) |
| 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)                |                                                                                                                                                                                 |
| bwa                | [github](https://github.com/lh3/bwa)                                                                                        | [publication](http://arxiv.org/abs/1303.3997)                                                                                                                                   |
| 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/)                                                                                           |                                                                                                                                                                                 |
| LEVIATHAN          | [github](https://github.com/morispi/LEVIATHAN)                                                                              | [publication](https://doi.org/10.1101/2021.03.25.437002)                                                                                                                        |
| LRez               | [github](https://github.com/morispi/LRez)                                                                                   | [publication](https://academic.oup.com/bioinformaticsadvances/article/1/1/vbab022/6375438?login=false)                                                                          |
| mamba              | [github](https://github.com/mamba-org/mamba)                                                                                |                                                                                                                                                                                 |
| Mimick             | [github](https://github.com/pdimens/mimick) [VISOR/XENIA](https://github.com/davidebolo1993/VISOR/tree/master/VISOR/XENIA)  |                                                                                                                                                                                 |
| NAIBR              | [github](https://github.com/raphael-group/NAIBR), [github (fork)](https://github.com/pontushojer/NAIBR)                     | [publication](https://doi.org/10.1093/bioinformatics/btx712)                                                                                                                    |
| plotly             | [website](https://plotly.com/)                                                                                              |                                                                                                                                                                                 |
| python             | [website](https://www.python.org/)                                                                                          |                                                                                                                                                                                 |
| QuickDeconvolution | [github](https://github.com/RolandFaure/QuickDeconvolution)                                                                 | [publication](https://doi.org/10.1093/bioadv/vbac068)                                                                                                                           |
| R                  | [website](https://www.r-project.org/)                                                                                       |                                                                                                                                                                                 |
| samtools           | [github](https://github.com/samtools/samtools), [website](http://www.htslib.org/)                                           |                                                                                                                                                                                 |
| seqtk              | [github](https://github.com/lh3/seqtk)                                                                                      |                                                                                                                                                                                 |
| simuG              | [github](https://github.com/aquaskyline/LRSIM)                                                                              | [publication](https://doi.org/10.1093/bioinformatics/btz424)                                                                                                                    |
| 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)                                                                                                                       |
| whatshap           | [github](https://github.com/whatshap/whatshap)                                                                              | [publication](https://doi.org/10.1101/085050)                                                                                                                                   |

## Software Packages
{.compact}
| Package     | Language | Links                                                                                                          | Publication                                        |
|:------------|:--------:|:---------------------------------------------------------------------------------------------------------------|:---------------------------------------------------|
| biocircos   |    R     | [github](https://github.com/lvulliard/BioCircos.R)                                                             |                                                    |
| click       |  python  | [github](https://github.com/pallets/click)                                                                     |                                                    |
| DT          |    R     | [website (R-package)](https://rstudio.github.io/DT/), [website (source)](http://datatables.net)                |                                                    |
| highcharter |    R     | [website (R-package)](https://github.com/jbkunst/highcharter/) [website (source)](https://www.highcharts.com/) |                                                    |
| pysam       |  python  | [github](https://github.com/pysam-developers/pysam)                                                            |                                                    |
| quarto      |    R     | [website](https://quarto.org/)                                                                                 |                                                    |
| rich        |  python  | [github](https://github.com/Textualize/rich)                                                                   |                                                    |
| rich-click  |  python  | [github](https://github.com/ewels/rich-click)                                                                  |                                                    |
| tidyverse   |    R     | [website](https://www.tidyverse.org/)                                                                          | [publication](https://doi.org/10.21105/joss.01686) |