The Pycnogonum litorale (Strøm, 1762) draft genome
This repository contains the computational analysis for the P. litorale draft genome manuscript. The code is split up by task, and should roughly correspond to the respective "Materials and Methods" sections of the manuscript.
- Assembly: code for read QC and genome assembly.
-
Scaffolding: code for scaffolding with
yahs. - Repeats: repeat prediction and annotation.
- Contam: analysis of repeats and possible contaminants; contaminant removal.
- Transcriptomes: de-novo assembly of deeply sequenced developmental transcriptomes.
- Annotation: prediction of protein-coding genes and tRNAs.
- Analysis: downstream analysis; placing P. litorale in the chelicerate/arthropod context, finding Hox genes, functional annotation with EggNOG-mapper.
- Submission: scripts to handle ENA submission.
The project's raw data can be found on ENA under project accession PRJEB80537. Additional (intermediate) results have been uploaded to Zenodo under the DOI 10.5281/zenodo.14185694.