Illumina sequence analysis was performed using the HGSC Mercury analysis pipeline [ 11] that manages all aspects of data processing and analyses, moving data step by step through various analysis tools from the initial sequence generation on the instrument to annotated variant calls (SNPs and intra-read in/dels).
PM participated in the concept and design of the study, was responsible of the supervision of data collection, data processing and analyses, and reviewed the paper.
GFM conceived the study and its design, was responsible of the supervision of data collection, data processing and analyses, and reviewed the paper.
RM participated in the concept and design of the study, was responsible of the supervision of the data collection, data processing and analyses, and reviewed the paper.
The authors gratefully acknowledge Prof. Emeritus J. Kasahara, and ex-members of Continental Shelf Surveys Co. Ltd., for data processing and analyses.
EL carried out all of the calculations, data processing and analyses, KS helped build datasets, and SJH designed experiments, drafted the manuscript and led the overall project.
Initial data processing and analyses were performed by K.C., R.K., D.R.K. and M.J.Z. with the guidance of A.M. and J.L.R. H.G. and E.K.S. generated WGBS libraries under the guidance of A.G. R.P. assisted with flow cytometry analysis.
Most data processing and genomic analyses of large-scale sequencing data are conducted on high-performance computing clusters running a UNIX-based operating system.
