PAQman is a tool for a reference-free and comprehensive evaluation of genome assemblies

fusemblr is a pipeline wrapper designed for the assembly of complex genomes using nanopore reads and paired-end illumina

This repository contains scripts/tools in order to detect Telomere-Linked-Repeats (TLRs)

A complete Starship and Starship-like region detection tool combining genome-graph based and starfish detection

Using de-novo assembly and read-phasing to assemble reference-free diploid genomes

MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (only v4) to detect Structural Variation

Describing the Starship repertoire of the Paecilomyces genus using 81 public genomes (2024)

A pipeline for Starship (or any large PAV) discovery using genome-graphs

Aneuploidy detection method for detecting both 'simple' and 'complex' aneuploidies

How to create a conda package with a new tool using the basis of a conda env already installed

functional enrichment of starship cargo versus non-cargo and between isolates of different origins

Data for keeping up to date UNESCO data with manually added sites visited by 1 or more individuals

Downloading sets of public genomes, analysing BUSCOs and generating trees for such genomes.

building a kraken2 db with public genomes but not the huge prebuilt databases

Small script designed to take a single genome assembly and identify contigs which show redundancy with large contigs through BLAST alignment