Software used in Harpy

A significant debt of gratitude; we stand on the shoulders of giants

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
arcs github, publication
athena github, publication
bash website
bcftools github, website
bwa github, publication
conda github
dmox gitlab
fastp github, publication
HapCUT2 github ,publication
htslib website
JupyterBook github, MyST
LEVIATHAN github ,publication
links github, publication
LRez github, publication
mamba github
Mimick github, VISOR/XENIA
NAIBR github, github (fork) ,publication
papermill github
python website
QuickDeconvolution github, publication
samtools github, website, publication
seqtk github
Snakemake github, publication
spades spades, cloudspades, spades, cloudspades
STITCH github, publication
strobealign github, publication
tigmint github, publication
whatshap github, publication
xeus-python github

Software Packages

Package Language Links
AG-Grid JavaScript github
altair Python/JavaScript github
click Python github
pandas Python github
vega-lite JavaScript github, publication
pysam Python github
numpy Python github
polars Python/Rust github
IPython Python/Rust github
rich Python github
rich-click Python github