microbial-genomics

There are 9 repositories under microbial-genomics topic.

pyCirclize
moshi4 / pyCirclize
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
bioinformatics circos matplotlib python chord-diagram comparative-genomics genomics genomics-visualization microbial-genomics visualization phylogenetic-trees data-visualization dataviz radar-chart
Language:Python 995
bakta
oschwengers / bakta
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
annotation bacteria bacterial-genomes bioinformatics genome-annotation mag metagenome-assembled-genomes microbial-genomics plasmids
Language:Python 564
ParBLiSS / FastANI
Fast Whole-Genome Similarity (ANI) Estimation
microbial-genomics
Language:C++ 435
pyGenomeViz
moshi4 / pyGenomeViz
A genome visualization python package for comparative genomics
bioinformatics comparative-genomics matplotlib microbial-genomics genomics genomics-visualization genbank python visualization synteny microbiology gff gff3
Language:Python 363
PPanGGOLiN
labgem / PPanGGOLiN
Build a partitioned pangenome graph from microbial genomes
comparative-genomics bioinformatics microbial-genomics microbiology bacteria pangenome
Language:Python 280
ANIclustermap
moshi4 / ANIclustermap
A tool for drawing ANI clustermap between all-vs-all microbial genomes
bioinformatics comparative-genomics genomics microbial-genomics phylogenetics phylogenomics python taxonomy visualization
Language:Python 85
COGclassifier
moshi4 / COGclassifier
A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
python bioinformatics cog genomics functional-annotation functional-analysis comparative-genomics visualization protein microbial-genomics genome-analysis
Language:Python 73
cmkobel / CompareM2
🦠🧬🧑‍💻📇 Microbial genomes-to-report pipeline
microbial-genomics snakemake genomes-to-report hpc conda apptainer bioinformatics pbs slurm bioconda prokaryotes metagenomics clinical-research archaea bacteria
Language:Python 72
hzi-bifo / traitar
From genomes to phenotypes: Traitar, the microbial trait analyzer
bioinformatics from-genome-to-phenotype metagenomics microbial-genomics microbial-trait-prediction
Language:Python 60
lmrodriguezr / nonpareil
Estimate metagenomic coverage and sequence diversity
bioinformatics microbial-genomics metagenomics
Language:C++ 56
Serka-M / mmlong2
Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes
bioinformatics long-read-sequencing metagenome-assembled-genomes metagenomics microbial-genomics microbiome nanopore pacbio
Language:Python 52
aleimba / bac-genomics-scripts
Collection of scripts for bacterial genomics
perl bioinformatics genomics science microbial-genomics microbiology ngs sequencing annotation mlst blast unix bioperl scripts-collection opensource computational-biology
Language:Perl 48
BeatsonLab-MicrobialGenomics / micropipe
A pipeline for high-quality bacterial genome construction using ONT sequencing
genome-assembly long-read-sequencing nanopore-analysis-pipeline bioinformatics-pipeline microbial-genomics oxford-nanopore
Language:HTML 39
MGCplotter
moshi4 / MGCplotter
Microbial Genome Circular plotting tool for comparative genomics using Circos
bioinformatics circos comparative-analysis comparative-genomics genomics genomics-visualization microbial-genomics molecular-evolution python visualization
Language:Python 38
bio-miga / miga
MiGA: Microbial Genomes Atlas
bioinformatics microbial-genomics genomics taxonomy
Language:Ruby 30
MDU-PHL / bohra
A pipeline for bioinformatics analysis of bacterial genomes
bioinformatics bioinformatics-pipeline mdu-phl microbial-genomics nextflow
Language:Nextflow 30
dinasv / CSBFinder
A Java Desktop application with a graphical user interface for the discovery of colinear syntenic blocks across thousands microbial genomes
gene-order gene-orthology microbial-genomics genomics pattern-mining synteny
Language:Java 29
iferres / pagoo
A comprehensive and intuitive encapsulated OO class system for analyzing bacterial pangenomes in R.
pangenome r rstats r6 microbial-genomics bioinformatics
Language:R 28
tseemann / seeka
Get microbial sequence data easier and faster
genomic-data downloader microbial-genomics life-changing-magic
Language:Perl 28
hallamlab / TreeSAPP
A Python package for gene-centric taxonomic and functional classification using phylogenetic placement
bioinformatics phylogenetics microbial-genomics
Language:Python 25
vallenderlab / MicrobiomeR
A comprehensive and customizable R package for microbiome analysis.
microbiome microbial-genomics microbiome-analysis phyloseq metacoder r rstats visualization color-palette bioinformatics permanova alpha-diversity beta-diversity pcoa comprehensive metagenomics microbiology
Language:R 23
moshi4 / pybarrnap
Python implementation of barrnap (Bacterial ribosomal RNA predictor)
bioinformatics genome-annotation genomics microbial-genomics microbiology python rna
Language:Python 22
GBKviz
moshi4 / GBKviz
Easy-to-use web application for visualization and comparison of genomes in Genbank file
bioinformatics biopython comparative-genomics genbank genomics genomics-visualization microbial-genomics python streamlit visualization webapp
Language:Python 21
GeneGrouper
agmcfarland / GeneGrouper
CLI tool for finding gene clusters in many genomes and placing them in discrete groups based on gene content similarity.
bioinformatics bioinformatics-tool clustering genomics microbial-genomics visualization
Language:Python 19
mbhall88 / NanoVarBench
Evaluating Nanopore-based bacterial variant calling
bacteria benchmark bioinformatics illumina microbial-genomics nanopore variant-calling
Language:Python 19
iferres / MLSTar
An easy way of MLSTyping your genomes in R.
genome microbial-genomics mlst pubmlst r
Language:R 18
Serka-M / mmlong2-lite
Lightweight bioinformatics pipeline for microbial genome recovery
bioinformatics long-read-sequencing metagenome-assembled-genomes metagenomics microbial-genomics microbiome nanopore pacbio singularity-container snakemake-workflow
Language:Python 17
Sudaraka88 / LDWeaver
Genomewide Epistasis Analysis on Bacteria
bioinformatics bacterial-genome-analysis epistasis-analysis linkage-disequilibrium microbial-genomics
Language:R 15
smdabdoub / phylotoast
Tools for phylogenetic data analysis including visualization and cluster-computing support.
16s bioinformatics computational-biology cross-platform hpc microbial-genomics microbiome microbiome-analysis pbs phylogenetics python qiime slurm visualization
Language:Python 14
cumbof / MetaSBT
A scalable framework for automatically indexing microbial genomes and accurately characterizing metagenome-assembled genomes with Sequence Bloom Trees
genomes metagenome-assembled-genomes sequence-bloom-trees metagenomics bioinformatics microbial-genomics
Language:Python 13
cidgoh / bacpaq
Bacterial Genomics workflow for short(Illumina) and long-read (Oxford Nanopore) sequencing data
bioinformatics microbial-genomics nextflow
Language:Nextflow 12
giffordlabcvr / gluetools
An open, platform-independent software toolkit for storage and interpretation of sequence data, implemented in Java.
virus-evolution comparative-genomics sequence-analysis microbial-genomics genomics reproducible-research
Language:Java 12
LanLab / ShigEiFinder
Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies
bioinformatics genomics microbial-genomics
Language:Python 12
cidgoh / nf-ncov-voc
A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 or Mpox genomes. Workflow is developed in collaboration with VIRUS-MVP (https://github.com/cidgoh/VIRUS-MVP) which can be used to visualize the mutation profiles and functional annotations.
bioinformatics genomics sars-cov-2 microbial-genomics covid-19 nextflow virus variant-calling
Language:Python 9
quadram-institute-bioscience / albatradis
Comparative TraDIS analysis
tradis bioinformatics microbial-genomics transposon-mutagenesis genomics bioinformatics-pipeline infectious-diseases next-generation-sequencing research pathogen sequencing global-health
Language:Gnuplot 9
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
population-genomics comparative-genomics whole-genome-genotyping pan-genome-analysis bioinformatics genomics computational-biology antimicrobial-resistance bacterial-gwas antibiotic-resistance whole-genome-sequencing whole-genome-alignment genome-analysis parallel-programming association-studies microbial-genomics
Language:C++ 7