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

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

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

Fast in-silico normalization algorithm for NGS data

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

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).

MAGqual is a command line tool to evaluate the quality of metagenomic bins and generate recommended metadata in line with the MIMAG standards

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

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