# 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
EMA github publication
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