Make Picrust2 Output Analysis and Visualization Easier

Graph-based assembly phasing

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

Miscellaneous functions for metagenomic analysis.

The MG-RAST Backend -- the API server

Local version of the virus identification and analysis web server (tool set)

Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat

LRBinner is a long-read binning tool published in WABI 2021 proceedings and AMB.

StaG Metagenomic Workflow Collaboration

VirBot: a protein-based RNA virus detector for metagenomic data

The MG-RAST pipeline

This repository contains all CWL descriptions of the MGnify pipeline version 5.0.

Fast in-silico normalization algorithm for NGS data

Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets

Calculate confidence scores from Kraken2 output

MerCat: python code for versatile k-mer counting and diversity estimation for database independent property analysis for meta -ome data

Fast sequence vectorization for metagenomics analysis. Converts input sequences into oligonucleotide frequency vectors, fast!

iMAP v1.0 (Pre-release): Integrated Microbiome Analysis Pipeline

MerCat2: python code for versatile k-mer counting and diversity estimation for database independent property analysis for metaome data

Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).