# 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

Software	Links	Publication
ARCS suite	tigmint, arcs, links	tigmint, arcs, links
athena	github	publication
bash	website
bcftools	github, website
bwa	github	publication
conda	github
dmox	gitlab
fastp	github	publication
HapCUT2	github	publication
htslib	website
LEVIATHAN	github	publication
LRez	github	publication
mamba	github
Mimick	github VISOR/XENIA
NAIBR	github, github (fork)	publication
plotly	website
python	website
QuickDeconvolution	github	publication
R	website
samtools	github, website
seqtk	github
simuG	github	publication
Snakemake	github	publication
spades	spades, cloudspades	spades, cloudspades
STITCH	github	publication
strobealign	github	publication
whatshap	github	publication

# Software Packages

Package	Language	Links	Publication
biocircos	R	github
click	python	github
DT	R	website (R-package), website (source)
highcharter	R	website (R-package) website (source)
pysam	python	github
quarto	R	website
rich	python	github
rich-click	python	github
tidyverse	R	website	publication