microbiology 开源项目推荐（425 个）

moshi4 /pyGenomeViz

A genome visualization python package for comparative genomics

MrOlm /drep

Rapid comparison and dereplication of genomes

microbiome /microbiome

microbiome R package

labgem /PPanGGOLiN

Build a partitioned pangenome graph from microbial genomes

Binomica-Labs /SpliceCraft

Terminal-based plasmid map viewer, sequence editor, and cloning/mutagenesis workbench in pure Python

ikeda042 /PhenoPixel

PhenoPixel: A web-based bioimage analysis platform for bacterial single-cell microscopy analytics.

oschwengers /platon

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

msberends /AMR

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.

oschwengers /referenceseeker

Rapid determination of appropriate reference genomes.

qgeissmann /OpenCFU

An easy-to-use C++ application to count bacterial colonies (i.e. CFU).

EngqvistLab /Tome

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

vinuesa /get_phylomarkers

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches

genotoul-bioinfo /Binette

A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.

happykhan /BRIG

BRIG 是一款跨平台（Windows/Mac/Linux）应用程序，使用 BLAST 显示多个基因组的圆形对比图像。

rdpstaff /RDPTools

Collection of commonly used RDP Tools for easy building

aleimba /bac-genomics-scripts

Collection of scripts for bacterial genomics

BU-ISCIII /plasmidID

PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.

telatin /gan

📜 the Great Automatic Nomenclator — The Next Million Names for Archaea and Bacteria

dmnfarrell /teaching

scripts and notes for learning

mikeblazanin /gcplyr

wrangling and model-free analysis of microbial growth curve data in R