Successor of bwa-mem for short-read alignment

A structural variation pipeline for short-read sequencing

DPM: code and input files for the publication

Integrative pathway enrichment analysis of multivariate omics data

GREAT algorithm in Python

Draw forestplot in R

🧬 gget enables efficient querying of genomic reference databases

A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.

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

Code for doing minor analyses related to the IBDverse sc-eQTL propject

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

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

⚡ ♒ Rapid prokaryotic genome annotation

Build haplotye and generate figures

A haplotype analysis toolkit for natural variation study.

This repository contains scripts used in the manuscript "Massive expansion of human gut bacteriophage diversity"

Phage-Host Interaction Search Tool

Unified Human Gut Virome Catalog

A meta-analysis package for R

Genotype Imputation Pipeline for H3Africa

Organize your project into a research website

Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics using WGS

Mapping RNA-seq data to topologically associating domains (TADs)

ProkEvo - an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses.

A pipeline for high-quality bacterial genome construction using ONT sequencing