michoug

ggdist

Visualizations of distributions and uncertainty

ggVennDiagram

A 'ggplot2' implement of Venn Diagram.

iab2

An Introduction to Applied Bioinformatics, 2nd Edition

corncob

Count Regression for Correlated Observations with the Beta-binomial

hybracter

Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.

MetONTIIME

A Meta-barcoding pipeline for analysing ONT data in QIIME2 framework

gLM

Genomic language model predicts protein co-regulation and function

radEmu

r-code-review-checklist

A checklist template for R code review

tidyheatmaps

Heatmaps from Tidy Data

GenomeSPOT

Predict oxygen, temperature, salinity, and pH preferences of bacteria and archaea from a genome

fairy

alignment-free coverage calculation for metagenomic binning >100 times faster

nail

Nail is an Alignment Inference tooL

ufcg

UFCG: Universal Fungal Core Genes

ViPTreeGen

a command line tool for viral proteomic tree generation, part of the ViPTree project: http://www.genome.jp/viptree

Binette

A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.

AleRax

Gene tree - species tree reconciliation from gene tree distributions

mebs

Protocol for finding informative protein families and then using them to score omic samples

Eukfinder

Eukfinder: A pipeline to retrieve microbial eukaryote genomes from metagenomic sequencing data

EUKsemble

Pipeline for identification of eukaryotic contigs in metagenomic assemblies

mercat2

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

QSAP

viruses_classifier

deepgometa

MAGqual

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

Depolymerase-Predictor

Depolymerase Predictor (DePP) - A machine learning tool facilitating phage depolymerase discovery

DepoScope

A fine-tuned ESM-2 model to accurately detect phage depolymerases in their genomes.

ANNA16

This repository releases the model weights of ANNA16, an end-to-end, web-based tool that predicts 16S rRNA gene copy number (GCN) from 16S rRNA sequence.

varKoder

Tool for DNA barcoding based on variation in short k-mer frequencies

meta-thermo

The stand-alone version of Metagenomic Thermometer (http://metathermo.jp/).