Resources from: Disparate patterns of genetic divergence in three widespread corals across a pan-pacific environmental gradient highlights species-specific adaptation trajectories

The following files are contained in this repository:

README.Hume_et_al_2022.zenodov2.txt - This document.

scripts.Hume_et_al_2022.zenodov2.pdf - Contains the scripts, or locations of the scripts, used to conduct the data analyses detailed in the associated manuscript.

acknowledgements_local_authorities.Hume_et_al_2022.zenodov1.pdf - Acknowledgements of local authorities for the collection of samples used in the associated study.

TaraPacific_SST_timeseries_mean_productsV2mai2021.Hume_et_al_2022.zenodov1.csv - The historical temperature data set used for the RDA and Mantel tests.

Pocillopora_meandrina_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip - The Pocillopora SNPs referred to as 'raw' in the Methods of the associated manuscript. Compressed using genozip (https://genozip.readthedocs.io/index.html).

Pocillopora_meandrina_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip.md5 - md5 of the the Pocillopora raw SNPs.

Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'linked' in the Methods of the associated manuscript.

Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora linked SNPs.

Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'unlinked' in the Methods of the associated manuscript.

Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora unlinked SNPs.

Porites_lobata_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip - The Pocillopora SNPs referred to as 'raw' in the Methods of the associated manuscript. Compressed using genozip (https://genozip.readthedocs.io/index.html).

Porites_lobata_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip.md5 - md5 of the the Pocillopora raw SNPs.

Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'linked' in the Methods of the associated manuscript.

Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora linked SNPs.

Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'unlinked' in the Methods of the associated manuscript.

Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora unlinked SNPs.

PANAMA2021.raw.Hume_et_al_2022.zenodov2.vcf.gz - The Millepora SNPs referred to as 'raw' in the Methods of the associated manuscript.

PANAMA2021.raw.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Millepora raw SNPs.

Millepora_REF_orthologue_genes.Hume_et_al_2022.zenodov2.csv - The Millepora gene list referred to as 'target genes' in the Methods of the associated manuscript.

Mil_transcriptom.Hume_et_al_2022.zenodov2.fa.gz - The Millepora de novo assembled transcriptome.

Mil_transcriptom.Hume_et_al_2022.zenodov2.fa.gz.md5 - md5 of the Millepora de novo assembled transcriptome.

REFERENCES
Lan, D., et al. (2022) Genozip 14 - advances in compression of BAM and CRAM files (preprint) bioRxiv, doi:10.1101/2022.09.12.507582

Lan, D., et al. (2022) Genozip Dual-Coordinate VCF format enables efficient genomic analyses and alleviates liftover limitations (preprint) bioRxiv 10.1101/2022.07.17.500374

Lan, D (2021) The Variant Call Format - Dual Coordinates Extension (DVCF) Specification (preprint) doi:10.6084/m9.figshare.14685816

Lan, D., et al. (2021) Genozip: a universal extensible genomic data compressor Bioinformatics, 37, 2225–2230

Lan, D., et al. (2020) genozip: a fast and efficient compression tool for VCF files Bioinformatics, 36, 4091–4092