fast phage annotation program

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

k-mer based assembly evaluation

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

FastOMA is a scalable software package to infer orthology relationship.

Automatic and optimised consensus clustering of one or more heterogeneous datasets

An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.

Tools for Metagenomic Networks Analysis

Novelty-inclusive microbial community profiling of shotgun metagenomes

🌟🧬 GraphBin-Tk: assembly graph-based metagenomic binning toolkit

Pipeline for metabolic annotation of microbial genomes

Reorients assembled microbial sequences

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

A library for creating complex UpSet plots with ggplot2 geoms

Predict AMPs in (meta)genomes and peptides

AMPDeep: Hemolytic Activity Prediction of Antimicrobial Peptides using Transfer Learning

Generator and regressor neural networks for antimicrobial peptides

📊 Circular and Rectangular Manhattan Plot

Attentive deep learning model for antimicrobial peptide prediction

Phage annotations and predictions. A spae is a prediction or foretelling. We'll foretell you what your phage is doing!

Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.

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

A machine learning-based tool for predicting metabolic modules in incomplete bacterial genomes.

GEne Cluster prediction with COnditional random fields.

Genomic language model predicts protein co-regulation and function