Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

Rapid Profiling and Deconvolution Tool for Metagenomes

Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes

Lightweight bioinformatics pipeline for microbial genome recovery

Binnacle: Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins

A scalable framework for automatically indexing microbial genomes and accurately characterizing metagenome-assembled genomes with Sequence Bloom Trees

kMetaShot is an alignment-free taxonomic classifier based on k-mer/minimizer counting for MAGs

Reproducible hybrid metagenomics with MAG recovery and strain-level resolution

Easy to use Snakemake metagenomic pipeline that covers a) read-based analysis b) contig based analysis and c) MAG assembly and annotation using a broad set of ready to use and included public databases and annotators

Pan-genomics of metagenome-assembled genomes suffers from fragmentation and incompleteness

Human oral metagenome-assembly-genome

The Metagenome-Assembled Genome Inventory for Children (MAGIC)

MetaSBT public databases

clutering of MAGs (metagenome assembled genomes) into MGS (metagenomic species)

Detect PyPI supply chain attacks in Python packages with pattern scans and LLM-based false positive filtering

Script repository related to the data processing and analyses of the study: "Cold adaptation and horizontal gene transfer shape Antarctic sponge microbiomes".