Interactive phylogenetic tree viewer/editor

Veterinary Pathogenic E. coli database

Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database

SISTR (Salmonella In Silico Typing Resource) command-line tool

Simple Transparent End-To-End Automated Machine Learning Pipeline for Supervised Learning in Tabular Binary Classification Data

In silico prediction of E. coli serotype

A New, Interactive Approach to Learning Python

Structural variation caller using third generation sequencing

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

A tool for generating consensus long-read assemblies for bacterial genomes

A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.

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

A flexible pipeline for complete analysis of bacterial genomes

Finds SNP sites from a multi-FASTA alignment file

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

Rules to run Roary or PanPhlAn to build pangenome using Snakemake

A fast tool for hybrid genome assembly of long and short reads

Applied Computational Genomics Course at UU: Spring 2020

SPAdes Genome Assembler

🆔 Scan contig files against PubMLST typing schemes

🔎 💊 Mass screening of contigs for antimicrobial and virulence genes

⚡ ♒ Rapid prokaryotic genome annotation

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Fast Reference-Guided Scaffolding of Genome Assembly Contigs

Rapid large-scale prokaryote pan genome analysis

💾 📃 "Reads to report" for public health and clinical microbiology

This is a beginner's tutorial to Snakemake

🐍🍔 A beginner's guide to modular snakemake workflows.

RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag