README

This repository holds the code and the data used to run the analyses in:
López-Nandam EH, Albright R, Hanson EA, Sheets EA, Palumbi SR (2023). Mutations in coral soma and sperm imply lifelong stem cell renewal and cell lineage selection. Proceedings of the Royal Society B 290:20221766. DOI: 10.1098/rspb.2022.1766

In /scripts you can find the code used to process the data and generate figures.

in /genome_annotations you can find the code used to annotate the new, chromosome-level Acropora hyacinthus genome assembly.

In /datafiles you can find the .ann.txt files generated by the MatchVerifiedMutswithAnnotatedVCF.py step. These files are then read into the R scripts for further filtering to arrived at the final set of SNVs, and to generate figures (see README in /scripts for pipeline). 

The raw fastq files for this paper are accessioned at NCBI SRA under BioProject PRJNA707502 under accession numbers SAMN18207983-SAMN18208014. 

The new, chromosome-level genome assembly generated for this paper is also under BioProject PRJNA707502, with accession number GCA_020536085.1 (https://www.ncbi.nlm.nih.gov/assembly/GCA_020536085.1/). You can download the associated gff3, proteins fasta, and other annotation files for this assembly here: https://drive.google.com/drive/u/1/folders/15dh6eE8q850frTRVtglndXtzxSwj673g

You can see photos of the colony whose sperm we used for the genome assembly here: https://photos.app.goo.gl/VuGrU3cBjidoaRfq5