ARTIC Epi2me compatible workflow and reporting

Tools for working with primerbed files

Application for analysis of targeted metagenomics sequencing data. Intended for use with multiplexed Illumina short-read data generated after enrichment.

Visualize microbial evolution at the SNP level!

accurate LiftOver tool for new genome assemblies

Optimal sequence-to-graph alignment with recombinations

A fast, user-friendly analysis and evaluation toolkit for some DNA sequence classification tasks

Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs

A bioinformatic toolkit to align genome assemblies into pangenome graphs

Phage Annotation using Protein Structures

VIRULIGN: fast codon-correct alignment and annotation of viral genomes

Nail is an Alignment Inference tooL

Code underlying Fountain-Jones et al 2021

A package for designing compact and comprehensive capture probe sets.

Reference genomes for viral genomics

A tool to prepare files and run/monitor programmatic submissions to NCBI

hecatomb is a virome analysis pipeline for analysis of Illumina sequence data

A post alignment toolkit for refining pairwise/multiple alignment sequences.

Part1: fastq and bam processing and quality check. Part2: variant calling, filtering and annotation

User-friendly AI Interface (Supports Ollama, OpenAI API, ...)

SemiBin: metagenomics binning with self-supervised deep learning

A library of search functions for various projects at APL

An Ollama-powered LLM Slack bot.

Convert a FASTA alignment with ambiguous nucleotides to literal distance matrix

Repository for pan-spefic primers designed for tiled full genome sequencing or qPCR of viral pathogens. Pathogens include amongst others Hepatitis E virus, Hepatitis A virus, Poliovirus and SARS-CO…

Pipeline for detecting coinfection of SARS-CoV-2 variants.