Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.

A new high-resolution long-read metagenome assembler for even noisy reads

A Nextflow pipeline for Antimicrobial Resistatnce exploration in metagenomic samples

Compare the quality of multiple genomes, along with their annotations.

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes

Only The Best (Genome Assembly Tools)

Extensive de-novo TE Annotator

Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation

GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.

Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.

Assembly and intrahost/low-frequency variant calling for viral samples

A pipeline to investigate horizontal gene transfer from NGS data

Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.

Pipeline for the identification of (coding) gene structures in draft genomes.

UNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies

Surveillance of pathogens using population genomics and sequencing

Assembly and binning of metagenomes

ARG normalization by mapping to the ARO ontology.

Firefly III: a personal finances manager

High performance self-hosted photo and video management solution.

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