A newly developed metabolic modeling pipeline, SuperCC, which could simulate the performances of different microbiomes.

An AI Agent for Fully Automated Multi-omic Analyses

Machine Learning Framework to Identify Coral Bacteria Associated with Thermal Resilience

MICROPHERRET: MICRObial PHEnotypic tRait ClassifieR using machine lEarning Techniques

MetMiner: A user-friendly pipeline for large-scale plant metabolomics data analysis

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

🌐 The Internet OS! Free, Open-Source, and Self-Hostable.

Spacedrive is an open source cross-platform file explorer, powered by a virtual distributed filesystem written in Rust.

Harmonized annotation of microbial physiology

Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks

The simplist and fastest RNA-seq analysis pipeline for Pseudomonas aeruginosa (or any bacteria with a reference genome)

Processing pipeline for pan-genome visulization and exploration

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

HMMER: biological sequence analysis using profile HMMs

Fast genome and metagenome distance estimation using MinHash

🔬 ♌ Bacterial ribosomal RNA predictor

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

Antibiotic resistance prediction in minutes

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes. It provides two models,deepARG-SS and deepARG-LS.

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

🔎 💊 Mass screening of contigs for antimicrobial and virulence genes

Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Simulate metagenomic short reads from one or more populations.

Antimicrobial Resistance Identification By Assembly

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

GUI/CommandLine Tool Box for biologistists to utilize NGS data.