Reference-quality genome reconstruction from complex metagenomes (or bacterial isolates) using only Nanopore long reads or both long and short reads (hybrid strategy)

Interpretation and visualization of microbiome charts

ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.

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

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

Scripts for antiSMASH/MiBIG data extraction and manipulation

Detection of phage RBPs based on protein domains and machine learning

Analyzing and visualizing KEGG information using the grammar of graphics

R package and web app for spatial visualisation of admixture on a projected map

Unicycler based iterative hybrid assembly for high-quality MAG reconstruction from the enrichment system

Viral Integrations in Bacterial genomES

A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.

Dropbox Uploader is a BASH script which can be used to upload, download, list or delete files from Dropbox, an online file sharing, synchronization and backup service.

Providing up-to-date phage genome databases, metrics and useful input files for a number of bioinformatic pipelines.

Predict the function of phage hypothetical proteins using an LSTM model trained with Phage Synteny

Graph-based assembly phasing

Python script to upload bins and MAGs to ENA (European Nucleotide Archive)

Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

Visualize and annotate genomic coverage with ggplot2

Accurate identification of bacteriophages from metagenomic data using Transformer

Depth-weighted De-Mixing

ggplot2 extension allowing for plotting various geometries as side panels using the ggplot2 API

Pod5: a high performance file format for nanopore reads.

🔎 💊 Mass screening of contigs for antimicrobial and virulence genes

Efficient phylogenomic software by maximum likelihood

Phigaro is a scalable command-line tool for predicting phages and prophages

Contains a fasta format database of a large variety of mobile genetic elements and an annotation file

Virus Identification By iteRative ANnoTation

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes