main README drafted

README.md

-# plit-genome
-The scripts and pipelines for the P. litorale draft genome assembly (DOI: xxx)
+# 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.
+
+1. **Assembly:** code for read QC and genome assembly.
+2. **Scaffolding:** code for scaffolding with `yahs`.
+3. **Repeats:** repeat prediction and annotation.
+4. **Contam:** analysis of repeats and possible contaminants; contaminant removal.
+5. **Transcriptomes:** de-novo assembly of deeply sequenced developmental transcriptomes.
+6. **Annotation:** prediction of protein-coding genes and tRNAs.
+7. **Analysis:** downstream analysis; placing _P. litorale_ in the chelicerate/arthropod context,
+   finding Hox genes, functional annotation with EggNOG-mapper.
+8. **Submission:** scripts to handle ENA submission.
+
+The project's raw data can be found on ENA under project ID [](). Additional (intermediate) results
+have been uploaded to Zenodo under the DOI [10.5281/zenodo.14185694](10.5281/zenodo.14185694).
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