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ancientmetagenomedir

Repository containing lists of all published ancient metagenome samples (and related)

arg_ranker

biobakery

bioBakery tools for meta'omic profiling

cdhit

Automatically exported from code.google.com/p/cdhit

cgview_comparison_tool

The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.

checkm

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes

cobra

A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.

das_tool

DAS Tool

diamond

Accelerated BLAST compatible local sequence aligner.

drep

Rapid comparison and dereplication of genomes

eggnog-mapper

Fast genome-wide functional annotation through orthology assignment

emg-viral-pipeline

VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies

eukdetect

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

fetchngs

Pipeline to fetch metadata and raw FastQ files from public databases

ggkegg

Analyzing and visualizing KEGG information using the grammar of graphics

gtdbtk

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

humann

HUMAnN 2.0 is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).

iqtree2

NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org

kraken2

The second version of the Kraken taxonomic sequence classification system

krakentools

KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

mb-gan

Microbiome Simulation via Generative Adversarial Network

megahit

Ultra-fast and memory-efficient (meta-)genome assembler

metagenome

Metagenome analysis pipeline

metaphage

metawrap

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

mgv

Supporting code for uncultivated gut virus manuscript

microbiomestatplot

Interpretation and visualization of microbiome charts

ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

phanta

Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes