An analysis and visualization platform for 'omics data

Making BUSCO HMMs useable in Anvi'o.

An automated Anvi'o v9 Snakemake workflow for competitive metagenomic read recruitment. Resolves conserved sequence homologies to enable strain-level taxonomic profiling, population-level abundance estimation, and genome detection limits across environmental samples.

PanAnalyzer is a powerful and integrated bioinformatics pipeline designed to streamline the process of genome analysis, moving from raw sequencing data to sophisticated, interactive pangenome visualization.

A genome-resolved metagenomics pipeline replicating the Sharon et al. (2019) gut-brain axis study. Features MEGAHIT de novo co-assembly, Bowtie2 competitive read recruitment, and Anvi'o single-nucleotide variant (SNV) microdiversity profiling.

This repository contains the computational pipeline and scripts formulated to conduct a comprehensive pangenome analysis of 36 complete Streptococcus pneumoniae genomes utilizing the Anvi'o (v9) bioinformatics platform.

A comprehensive, automated pan-genomic analysis pipeline for Bacteroides species, utilizing the Anvi'o platform to resolve core and accessory genomic architectures and infer evolutionary dynamics.

A reproducible pangenomic analysis of seven Chlamydia trachomatis strains using anvi'o v9, exploring core and accessory gene clusters across different serovars and clinical isolates.

Species-level pangenomes of the human oral microbiome constructed from eHOMD genomes using Anvi’o and reproducible Snakemake workflows.

This pipeline implements competitive fragment recruitment to map metagenomic sequence space against a representative reference genome. In microbial ecology, read recruitment provides a quantitative window into the evolutionary dynamics of natural populations by measuring nucleotide-level polymorphism and consensus sequence divergence.

Pangenomic analysis of Vibrio jasicida using the anvi'o platform. Identifies 6,853 gene clusters across eight genomes via DIAMOND and MCL clustering, resolving core, accessory, and strain-specific gene content.