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The Top 23 Microbiology Open Source Projects

Open source projects categorized as Microbiology
Categories > Microbiology
Microbiome ⭐ 257
microbiome R package
most recent commit 10 months ago
Drep ⭐ 199
Rapid comparison and dereplication of genomes
dependent packages 1total releases 63most recent commit 8 months agopypi drep} Downloads
Ppanggolin ⭐ 191
Build a partitioned pangenome graph from microbial genomes
total releases 6most recent commit 4 months ago
Pygenomeviz ⭐ 177
A genome visualization python package for comparative genomics
dependent packages 1total releases 23most recent commit 7 months agopypi pygenomeviz} Downloads
Platon ⭐ 93
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
total releases 10most recent commit 8 months ago
Referenceseeker ⭐ 85
Rapid determination of appropriate reference genomes.
total releases 12most recent commit 4 months ago
Amr ⭐ 74
Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in https://doi.org/10.18637/jss.v104.i03.
total releases 27most recent commit 6 months ago
Get_phylomarkers ⭐ 39
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
most recent commit a year ago
Rdptools ⭐ 36
Collection of commonly used RDP Tools for easy building
most recent commit 3 years ago
Scripts ⭐ 33
Metagenomic pipeline and other general scripts used in the lab.
most recent commit 2 years ago
Bac Genomics Scripts ⭐ 28
Collection of scripts for bacterial genomics
most recent commit 4 years ago
Ghost Tree ⭐ 23
creating hybrid-gene phylogenetic trees for diversity analyses
most recent commit 2 years ago
Plasmidid ⭐ 22
PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.
most recent commit 3 years ago
Idbacapp ⭐ 20
A MALDI Mass Spectrometry Bioinformatics Platform
most recent commit 2 years ago
Phantasm ⭐ 20
PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes
most recent commit 6 months ago
Microbiomer ⭐ 17
A comprehensive R package for microbiome analysis.
most recent commit a year ago
Gambit ⭐ 16
A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.
most recent commit 6 months ago
Hamroaster ⭐ 15
hAMRoaster is an analysis pipeline that can compare the output of nine different tools for detecting AMR genes and provide metrics of their performance
most recent commit 2 years ago
Kg Microbe ⭐ 14
most recent commit 4 months ago
Onepetri ⭐ 11
Accelerate common Petri dish assays with AI.
most recent commit a year ago
Tome ⭐ 9
A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima
most recent commit 4 years ago
Mgkit ⭐ 8
MGKit: Metagenomics Framework
most recent commit 2 years ago
Bacdiver ⭐ 8
Inofficial R client for the DSMZ's Bacterial Diversity Metadatabase (former contact: @katrinleinweber). https://api.bacdive.dsmz.de/client_examples seems to be the official alternatives.
most recent commit 2 years ago
The 2 Most Depended On Microbiology Open Source Projects
Drep ⭐ 199
Rapid comparison and dereplication of genomes
dependent packages 1total releases 63latest release September 15, 2023most recent commit 8 months agopypi drep} Downloads
Pygenomeviz ⭐ 177
A genome visualization python package for comparative genomics
dependent packages 1total releases 23latest release October 28, 2023most recent commit 7 months agopypi pygenomeviz} Downloads
The 6 Latest Releases In Microbiology Open Source Projects
Pygenomeviz ⭐ 177
A genome visualization python package for comparative genomics
dependent packages 1total releases 23latest release October 28, 2023most recent commit 7 months agopypi pygenomeviz} Downloads
Drep ⭐ 199
Rapid comparison and dereplication of genomes
dependent packages 1total releases 63latest release September 15, 2023most recent commit 8 months agopypi drep} Downloads
Platon ⭐ 93
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
total releases 10latest release August 10, 2023most recent commit 8 months ago
Referenceseeker ⭐ 85
Rapid determination of appropriate reference genomes.
total releases 12latest release January 14, 2022most recent commit 4 months ago
Ppanggolin ⭐ 191
Build a partitioned pangenome graph from microbial genomes
total releases 6latest release July 15, 2018most recent commit 4 months ago
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