microbial-genomics
There are 127 repositories under microbial-genomics topic.
moshi4/pyCirclize
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
oschwengers/bakta
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
ParBLiSS/FastANI
Fast Whole-Genome Similarity (ANI) Estimation
moshi4/pyGenomeViz
A genome visualization python package for comparative genomics
labgem/PPanGGOLiN
Build a partitioned pangenome graph from microbial genomes
moshi4/ANIclustermap
A tool for drawing ANI clustermap between all-vs-all microbial genomes
moshi4/COGclassifier
A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
hzi-bifo/traitar
From genomes to phenotypes: Traitar, the microbial trait analyzer
cmkobel/CompareM2
🦠📇 Microbial genomes-to-report pipeline
lmrodriguezr/nonpareil
Estimate metagenomic coverage and sequence diversity
aleimba/bac-genomics-scripts
Collection of scripts for bacterial genomics
Serka-M/mmlong2
Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes
BeatsonLab-MicrobialGenomics/micropipe
A pipeline for high-quality bacterial genome construction using ONT sequencing
moshi4/MGCplotter
Microbial Genome Circular plotting tool for comparative genomics using Circos
bio-miga/miga
MiGA: Microbial Genomes Atlas
dinasv/CSBFinder
A Java Desktop application with a graphical user interface for the discovery of colinear syntenic blocks across thousands microbial genomes
iferres/pagoo
A comprehensive and intuitive encapsulated OO class system for analyzing bacterial pangenomes in R.
tseemann/seeka
Get microbial sequence data easier and faster
hallamlab/TreeSAPP
A Python package for gene-centric taxonomic and functional classification using phylogenetic placement
moshi4/GBKviz
Easy-to-use web application for visualization and comparison of genomes in Genbank file
vallenderlab/MicrobiomeR
A comprehensive and customizable R package for microbiome analysis.
MDU-PHL/bohra
A pipeline for bioinformatics analysis of bacterial genomes
agmcfarland/GeneGrouper
CLI tool for finding gene clusters in many genomes and placing them in discrete groups based on gene content similarity.
iferres/MLSTar
An easy way of MLSTyping your genomes in R.
mbhall88/NanoVarBench
Evaluating Nanopore-based bacterial variant calling
moshi4/pybarrnap
Python implementation of barrnap (Bacterial ribosomal RNA predictor)
smdabdoub/phylotoast
Tools for phylogenetic data analysis including visualization and cluster-computing support.
Sudaraka88/LDWeaver
Genomewide Epistasis Analysis on Bacteria
giffordlabcvr/gluetools
An open, platform-independent software toolkit for storage and interpretation of sequence data, implemented in Java.
LanLab/ShigEiFinder
Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies
quadram-institute-bioscience/albatradis
Comparative TraDIS analysis
Serka-M/mmlong2-lite
Lightweight bioinformatics pipeline for microbial genome recovery
MDU-PHL/LisSero
In silico serotype prediction for Listeria monocytogenes
KiranJavkar/PRAWNS
PRAWNS: A fast and scalable bioinformatics tool that generates an efficient pan-genome representation of closely related whole genomes to provide a concise list of genomic features
cidgoh/nf-ncov-voc
A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 genomes (Variants of Concern and Variants of Interest). Workflow is developed in collaboration with COVID-MVP (https://github.com/cidgoh/COVID-MVP) which can be used to visualize the mutation profiles and functional annotations.