This GitHub repository contains links to data and scripts used for a meta-analysis of Pocillopora coral transcriptome data. This analysis was presented as a poster "Towards a modern integrative taxonomy of Pocillopora corals: a literature synthesis and meta-analysis of genetic data" (#3964) at Ocean Sciences Meeting 2022.

Pocillopora RNAseq studies used in meta-analysis

Study	NCBI SRA Link
Vidal-Dupiol et al. 2014	https://www.ncbi.nlm.nih.gov/sra/SRP029998
Yuan et al. 2017	https://www.ncbi.nlm.nih.gov/sra/PRJNA299443
Zhou et al. 2017	https://www.ncbi.nlm.nih.gov/sra/PRJNA327142
Brener-Raffali et al. 2018	https://www.ncbi.nlm.nih.gov/sra/PRJNA399069
Delgadillo-Nuño et al. 2018	https://www.ncbi.nlm.nih.gov/sra/PRJNA552592
Tang et al. 2018	https://www.ncbi.nlm.nih.gov/sra/PRJNA433950
Wecker et al. 2018	https://www.ncbi.nlm.nih.gov/sra/PRJNA369135
Zhou et al. 2018	https://www.ncbi.nlm.nih.gov/sra/PRJNA401252
Poquita-Du et al. 2019	https://www.ncbi.nlm.nih.gov/sra/PRJNA435468
Zhou et al. 2019	https://www.ncbi.nlm.nih.gov/sra/PRJNA435620
Buitrago-Lopez et al. 2020	https://www.ncbi.nlm.nih.gov/sra/PRJNA551401
Chuang & Mitarai 2020	https://www.ncbi.nlm.nih.gov/sra/PRJNA595781
Li et al. 2020	https://www.ncbi.nlm.nih.gov/sra/PRJNA559028
Connelly et al. 2020	https://www.ncbi.nlm.nih.gov/sra/PRJNA587509
Connelly et al. 2022	https://www.ncbi.nlm.nih.gov/sra/PRJNA587509
Grupstra et al. 2022	https://www.ncbi.nlm.nih.gov/sra/PRJNA778019

*studies using larvae, bailed-out polyps and 3’ tagged libraries were excluded this analysis.

For a comprehensive table of Pocillopora population genetics studies since 1984 (not including RNAseq studies), please see "pocillopora_popgen_studies.csv""

The meta-analysis approach involved read quality control and trimming, alignment to the P. damicornis reference genome, followed by the Genome Analysis Toolkit RNAseq variant calling best practices pipeline.