Manuscript reference: Bongaerts P, Riginos C, Brunner R, Englebert N, Smith SR, Hoegh-Guldberg O (2016) Deep reefs are not universal refuges: reseeding potential varies among coral species. Science Advances 3:e1602373 [DOI: 10.1126/sciadv.1602373]
Electronic lab notebook author: Pim Bongaerts
A - Symbiodinium - Details the analysis of the sequence data for the FACS-isolated Symbiodinium that are used as subtraction datasets.
B - Agaricia - Details the processing and analyses of the Agaricia fragilis dataset, from raw sequences to eventual population genomic analyses.
C - Stephanocoenia - Details the processing and analyses of the Stephanocoenia intersepta dataset, from raw sequences to eventual population genomic analyses.
D - Figures - Contains the data and scripts to produce the manuscript figures.
E - Scripts - Several custom scripts (other than those in RADseq script library) specific to the analysis of the Bermuda dataset.
F - Protocols - Details the lab protocols for gDNA isolation and fluorescence-activated cell sorting.
Raw sequence data (NCBI SRA) - Raw Illumina sequence data (fastq format) for the 109 Stephanocoenia intersepta and 104 Agaricia fragilis coral colonies sequenced in this study (accession code PRJNA361144).
RADseq script library (GitHub) - Separate github repository with generic Python scripts used throughout the electronic lab notebook (A-C).
Fieldwork Photos (Gallery) - Several photos of the fieldwork in Bermuda
Each (sub)heading in the electronic notebooks (listed above) refers to a directory in the repository, outlining the analysis workflow in sequential order.
Files are marked with a code referring to the directory/step where they were generated. In the example below, the input file afra_2b.vcf was produced in the step/directory B2b - Basic SNP QC and filtering, and the output file of this step/directory B2c - Check for clones is labeled afra_2c.vcf.
Besides the Python scripts in the separate RAD - Python scripts repository, the analyses depend on the following packages that need to be accessible through the PATH environmental variable:
| Package | Version (used) | Type | Note |
|---|---|---|---|
| PyRAD | 3.0.6 | Python Application | requires: numpy, scipy, muscle and vsearch |
| PyVCF | 0.6.7 | Python Module | |
| NumPy | 1.11.1 | Python Package | |
| BioPython | 1.67 | Python Package | |
| vcfR | 1.2.0 | R Package | |
| hierfstat | 0.04-22 | R Package | |
| adegenet | 2.0.1 | R Package | |
| BLAST+ | 2.5.0 | Executable (CL) | (older versions no longer support remote db connect) |
| VCFtools | 0.1.15 | Executable (CL) | |
| PGDSpider | 2.0.5.1 | Executable (CL/GUI) | used with a command-line wrapper |
| Arlecore | 3.5.2.2 | Executable (CL) | part of Arlequin package |
| Lositan | 1.0.0 | Executable (GUI) | |
| BayeScan | 2.1 | Executable (CL) | |
| STRUCTURE | 2.3.4 | Executable (CL/GUI) | used with a multi-threading wrapper |
Additional R packages used for plotting [figures](D - Figures/README.md): ggplot2, reshape2, gridExtra, cowplot, plyr