Bacterial_genomics_software_tools

A very non-exhaustive curated list of software tools for various aspects of prokaryote genomic analyses - mostly command line tools. For online options, please see: https://github.com/zadyson/Online-genomics-software-tools. Please note I am not affiliated with these tools, unless otherwise stated, nor have I explored their full functionality.

Gene screening (e.g. AMR, virulence, plasmids)

SRST2: https://github.com/katholt/srst2
ARIBA: https://github.com/sanger-pathogens/ariba
AbritAMR ISO acredited AMR detection pipeline for public health labs: https://github.com/MDU-PHL/abritamr

Plasmids

MOB-suite: https://github.com/phac-nml/mob-suite PLSDB: https://ccb-microbe.cs.uni-saarland.de/plsdb

Prophages

VIR-sorter: https://github.com/simroux/VirSorter
VIR-sorter2: https://github.com/jiarong/VirSorter2
ViPTreeGen: https://github.com/yosuken/ViPTreeGen

Insertion Sequneces

ISMapper: https://github.com/jhawkey/IS_mapper

CRISPR-Cas

CRISPR Comparison ToolKit (CCTK): https://github.com/Alan-Collins/CRISPR_comparison_toolkit
CRISPRCasFinder: https://crisprcas.i2bc.paris-saclay.fr/Home/Download
CRISPR Visualiser: github.com/CRISPRlab/CRISPRviz
CRISPRdisco: http://github.com/crisprlab/CRISPRdisco CRISPR-Detector: https://github.com/hlcas/CRISPRdetector
CRIPSR Recognition Tool (CRT): http://www.room220.com/crt
PILER-CR: http://www.drive5.com/pilercr

Mapping and variant calling

snippy; https://github.com/tseemann/snippy
RedDog: https://github.com/katholt/RedDog
ParSNP: https://harvest.readthedocs.io/en/latest/content/parsnp.html

Phylogenetic inference:

RAxML: https://github.com/stamatak/standard-RAxML
FastTree: http://www.microbesonline.org/fasttree/
iqtree: http://www.iqtree.org/

Phylodynamics

BEAST: https://beast.community/
BEAST2: https://www.beast2.org/
TreeDater: https://github.com/emvolz/treedater
BactDating: https://github.com/xavierdidelot/BactDating
Skygrowth: https://github.com/mrc-ide/skygrowth
Treemer: https://git.scicore.unibas.ch/TBRU/Treemmer
TipDatingBEAST: https://github.com/cran/TipDatingBeast

Clustering

PopPUNK: https://poppunk.net/
HierBAPS: https://github.com/gtonkinhill/rhierbaps
FastBAPS: https://github.com/gtonkinhill/fastbaps

LD

Lian: http://guanine.evolbio.mpg.de/cgi-bin/lian/lian.cgi.pl
Ia measure via Poppr: https://grunwaldlab.github.io/poppr/reference/poppr-package.html

Haplotype networks

popART: https://github.com/jessicawleigh/popart.

Typing

MLST: https://github.com/tseemann/mlst
Mykrobe: https://github.com/Mykrobe-tools/mykrobe

Transmission chain reconstruction

Transphylo: https://github.com/xavierdidelot/TransPhylo
Outbreaker2: https://github.com/reconhub/outbreaker2

Assembly

Unicycler: https://github.com/rrwick/Unicycler
SPAdes: https://github.com/ablab/spades

Annotation

PROKKA: https://github.com/tseemann/prokka
Bakta: https://github.com/oschwengers/bakta

Pangenome

Roary: https://sanger-pathogens.github.io/Roary/
Panstripe: https://github.com/gtonkinhill/panstripe/

Microbiome (16S)

QIIME2: https://qiime2.org/
DESeq2: https://joey711.github.io/phyloseq-extensions/DESeq2.html

Read and assembly manipulation

Fastaq: https://github.com/sanger-pathogens/Fastaq

PCR primer design and validation

RUCS: https://bitbucket.org/genomicepidemiology/rucs/src/master/
PrimerBLAST: https://www.ncbi.nlm.nih.gov/tools/primer-blast/
MFEPrimer: https://mfeprimer3.igenetech.com/specificity

In silico PCR

https://anaconda.org/bioconda/ispcr

Machine learning from WGS

GenoLearn: https://genolearn.readthedocs.io/en/latest/

Growth curve analysis:

Growthcurver: https://github.com/sprouffske/growthcurver