This repository contains the scripts used to assemble and analyze the first two genomes of Nematomorpha. If you use this repository, please cite:
Cunha TJ, de Medeiros BAS, Lord A, Sørensen MV, Giribet G. 2023. Rampant loss of universal metazoan genes revealed by a chromosome-level genome assembly of the parasitic Nematomorpha. Current Biology 33, https://doi.org/10.1016/j.cub.2023.07.003
The assemblies were built with long reads from Oxford Nanopore Technologies, and with Illumina short reads from whole-genome and Hi-C libraries.
Assembly Pipeline: instructions and scripts used to assemble genomes.
Annotation: scripts used to annotate genomes.
BUSCO and Enrichment Analyses: R code for busco comparison, enrichment analyses, and related figures.
Synteny Plot: instructions and scripts for synteny analysis and plotting.
Non-coding Distances: R code for comparison of intron sizes and intergenic distances.