bacterial-genomes
There are 84 repositories under bacterial-genomes topic.
tseemann/prokka
:zap: :aquarius: Rapid prokaryotic genome annotation
oschwengers/bakta
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
bactopia/bactopia
A flexible pipeline for complete analysis of bacterial genomes
gem-pasteur/Integron_Finder
Bioinformatics tool to find integrons in bacterial genomes
simonrharris/SKA
Split Kmer Analysis
nf-core/bacass
Simple bacterial assembly and annotation pipeline
esteinig/sketchy
Genomic neighbor typing of bacterial pathogens using MinHash :rat:
BioinformaticsLabAtMUN/Promotech
Machine-learning-based general bacterial promoter prediction tool.
jordanlab/stringMLST
Fast k-mer based tool for multi locus sequence typing (MLST)
paulstothard/cgview
CGView is a Java package for generating high-quality, zoomable maps of circular genomes.
liaoherui/StrainScan
High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers
telatin/gan
📜 the Great Automatic Nomenclator — The Next Million Names for Archaea and Bacteria
paulstothard/cgview_comparison_tool
The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.
refresh-bio/PHIST
Phage-Host Interaction Search Tool
wanyuac/GeneMates
An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
metageni/Scaffold_builder
Combining de novo and reference-guided assembly with Scaffold_builder
apredeus/10k_genomes
Various scripts for efficient processing of 10k Salmonella genomes
milnus/Magphi
Tool intended to pull out sequences and annotations between insertion sites specified by the user.
niu-lab/gclust
genome sized sequences clustering
zhaoc1/nanoflow
Bioinformatics pipeline for nanopore sequencing data
francesccoll/powerbacgwas
PowerBacGWAS: Power calculations for Bacterial GWAS
rx32940/BactPrep
Flexible workflow designed for bacterial WGS analyses (annotation, core/pan-genome reconstruction, phylogeny)
lmc297/seq2mlst
In silico multi-locus sequence typing (MLST) for bacterial genomes
tseemann/noary
🍣 🦐 A lightweight nucleotide bacterial ortholog clustering tool
BU-ISCIII/taranis
cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.
jime-sg/deleat
DELEAT is a bioinformatic analysis pipeline for the design of large-scale genome deletions in bacterial genomes.
lmc297/BTyper
Rapid, in silico characterization of Bacillus cereus group isolates using WGS data
lmc297/SNPBac
SNP and variant calling pipeline for bacteria
charlesrocabert/Evo2Sim
Digital evolution model dedicated to bacterial in silico experimental evolution.
Snitkin-Lab-Umich/prewas
R package to perform data pre-processing for more informative bacterial GWAS
infinity-a11y/PhyloTrace
PhyloTrace is a GUI platform for a fully controllable cgMLST analysis workflow.
mbhall88/thesis
My PhD thesis
molevol-ub/BacterialDuplicates
Identification of putative duplicated genes among bacterial genomes
tseemann/injecta
Insert genes into genomes to aid synthetic test data generation
bioinfoUQAM/Caribou
Alignment-free bacterial identification and classification in metagenomics sequencing data using machine learning
NotTheStallion/Computer-vision-in-the-service-of-bacteriology
Computer vision in the service of bacteriology refers to the use of computer algorithms and technology to analyze and interpret images of bacteria for the purpose of identifying and characterizing different types of bacteria.