Bacterial-Genomics-Tools-and-Packages

Welcome! This repo to create a central place of all the tools and packages I've used for much of my genomic research. Many are mostly bacterial oriented, but some can be used for nearly any organism. If you'd like to add a tool to this list, feel free to submit an issue and if it looks appropriate, I will add it.

All tools Illumina Reads

Package/Tool	Reference (DOI)	Guide	Install/Language	Github/CRAN
bbtools	N/A?	My Guide	conda/java	??
fastp	10.1093/bioinformatics/bty560	Guide	conda/C++	https://github.com/OpenGene/fastp

Genome(s) Comparison

Package/Tool	Reference (DOI)	Guide	Install/Language	Github
minimap2	10.1093/bioinformatics/bty191	Guide	conda/C	https://github.com/lh3/minimap2#uguide
pafr	N/A	Guide	Devtools/R	https://github.com/dwinter/pafr
fastANI	10.1038/s41467-018-07641-9	Guide	conda/C++	https://github.com/ParBLiSS/FastANI
sourmash	10.21105/joss.00027	Guide	conda/python&rust	https://github.com/dib-lab/sourmash
ggbio	10.1186/gb-2012-13-8-r77	Guide	bioconductor/R	bioconductor link

Gene(s) Comparison

Package/Tool	Reference (DOI)	Guide	Install/Language	Github
clinker	10.1101/2020.11.08.370650	TBD	pip/python	https://github.com/gamcil/clinker
gggenes	N/A	Guide	cran&Devtools/R	https://github.com/wilkox/gggenes
gggenomes	N/A	Guide	Devtools/R	https://github.com/thackl/gggenomes/

Pangenomes

Package/Tool	Reference (DOI)	Guide	Install/Language	Github
PPanGGOLiN	10.1371/journal.pcbi.1007732	TBD	conda/C	https://github.com/labgem/PPanGGOLiN

Phylogenomics

Package/Tool	Reference (DOI)	Guide	Install/Language	Github
TreeIO	10.1093/molbev/msz240.	Guide	BioCManager/R	https://github.com/YuLab-SMU/treeio
ggTree	10.1111/2041-210X.12628	Guide	cran/R	https://github.com/YuLab-SMU/ggtree

Population Genetics

Package/Tool	Reference (DOI)	Guide	Install/Language	Github
poppr	10.3389/fgene.2015.00208	Guide	cran/R	https://github.com/grunwaldlab/poppr

Other Useful Packages

Package/Tool	Reference (DOI)	Guide	Install/Language	Github
evobiR	10.5281/zenodo.30938	Guide	cran&Devtools/R	https://github.com/coleoguy/evobir