bacteria

Star

Here are 212 public repositories matching this topic...

Language:All

Filter by language

All212 Python69 R31 Jupyter Notebook17 JavaScript13 Shell12 HTML9 Perl7 Nextflow7 MATLAB6 C#3

Sort:Most stars

Sort options

Most stars Fewest stars Most forks Fewest forks Recently updated Least recently updated

Ecogenomics /GTDBTk

Star505

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

bioinformatics nomenclature taxonomy metagenomics phylogenetics bacteria archaea species-assignments

UpdatedMar 5, 2025
Python

tseemann /snippy

Star499

✂️ ⚡ Rapid haploid variant calling and core genome alignment

bioinformatics snps genomics vcf variant-calling bacteria indel-discovery haploid fastq-analysis

UpdatedJul 19, 2024
Perl

oschwengers /bakta

Star489

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

mag bioinformatics annotation genome-annotation microbial-genomics bacteria plasmids bacterial-genomes metagenome-assembled-genomes

UpdatedMar 11, 2025
Python

labgem /PPanGGOLiN

Star261

Build a partitioned pangenome graph from microbial genomes

bioinformatics microbial-genomics microbiology comparative-genomics bacteria pangenome

UpdatedMar 13, 2025
Python

AdmiralenOla /Scoary

Star191

Pan-genome wide association studies

gwas genomics bacteria pan-genome gene-presence-absence

UpdatedMay 29, 2024
Python

B-UMMI /chewBBACA

Star141

BSR-Based Allele Calling Algorithm

bioinformatics genomics mlst bacteria cgmlst outbreak-detection wgmlst bacterial-genome-analysis allele-calling bacterial-typing

UpdatedMar 11, 2025
HTML

tseemann /nullarbor

Star139

💾 📃 "Reads to report" for public health and clinical microbiology

public-health report variant-calling bacteria fastq phylogenomics denovo-assembly genotyping resistome virulome

UpdatedMar 19, 2024
Perl

mgalardini /pyseer

Star120

SEER, reimplemented in python 🐍🔮

gwas reproducible-science reimplementation bacteria k-mer

UpdatedOct 23, 2024
Python

oschwengers /platon

Star114

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

bioinformatics assembly ngs microbiology bacteria wgs contigs plasmids

UpdatedJan 22, 2025
Python

eead-csic-compbio /get_homologues

Star113

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

annotation clustering plants genbank fasta bacteria transcriptome pangenome pangene

UpdatedMar 3, 2025
Perl

Pioreactor /pioreactor

Star108

Hardware and software for accessible, extensible, and scalable bioreactors. Built on Raspberry Pi.

science mqtt raspberry-pi hardware biology raspberrypi evolution educators bacteria algae fermentation yeast biotech bioreactor

UpdatedMar 18, 2025
Python

neherlab /pangraph

Star101

A bioinformatic toolkit to align genome assemblies into pangenome graphs

bioinformatics genome julia bacteria genome-assembly pangenome pangraph

UpdatedMar 17, 2025
C

bacpop /PopPUNK

Star97

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

genomics sketching bacteria k-mer population-genetics

UpdatedMar 18, 2025
Python

oschwengers /asap

Star73

A scalable bacterial genome assembly, annotation and analysis pipeline

bioinformatics annotation assembly ngs amr bacteria

UpdatedDec 5, 2023
Groovy

kjolley /BIGSdb

Star67

Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.

bioinformatics database typing mlst bacteria genomes

UpdatedMar 18, 2025
Perl

cmkobel /CompareM2

Star56

🦠📇 Microbial genomes-to-report pipeline

bioinformatics snakemake hpc slurm conda metagenomics bioconda microbial-genomics bacteria clinical-research pbs prokaryotes archaea genomes-to-report apptainer

UpdatedMar 5, 2025
Python

EngqvistLab /Tome

Star55

A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima

machine-learning bioinformatics microbiology bacteria temperature-data eukaryotes archaea enzymes

UpdatedSep 30, 2020
Python

nf-core /bactmap

Star53

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

workflow tree pipeline genomics nextflow mapping bacteria phylogeny bacterial nf-core bacterial-genome-analysis

UpdatedMar 13, 2025
Nextflow

voorloopnul /awesome-phages

Star48

A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.

bioinformatics bacteria phages bacteriophages

UpdatedJul 12, 2022

johnlees /seer

Star43

sequence element (kmer) enrichment analysis

gwas bacteria k-mer

UpdatedNov 7, 2022
C++

Improve this page

Add a description, image, and links to thebacteria topic page so that developers can more easily learn about it.

Curate this topic

Add this topic to your repo

To associate your repository with thebacteria topic, visit your repo's landing page and select "manage topics."

Learn more

Movatterモバイル変換

Navigation Menu

Search code, repositories, users, issues, pull requests...

Provide feedback

Saved searches

Use saved searches to filter your results more quickly