MMseqs2: ultra fast and sensitive search and clustering suite
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
Versatile open-source tool for microbiome analysis
Ultra-fast and memory-efficient (meta-)genome assembler
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Accurate sample inference from amplicon data with single nucleotide resolution
An analysis and visualization platform for 'omics data
A complete pipeline for metagenomic analysis
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
ATLAS - Three commands to start analyzing your metagenome data
A collection of Galaxy-related training material
Rapid comparison and dereplication of genomes
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.
Assembly and binning of metagenomes
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.
Amplicon sequencing analysis workflow using DADA2 and QIIME2
🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
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