Things you will find…..
1 Genome Sequencing and Assembly: Significant efforts are dedicated to assembling and annotating the genomes of various marine species, notably the Pacific geoduck and Olympia oyster. This includes using different sequencing technologies (Illumina, PacBio) and assembly tools.
2 Transcriptome Analysis: The notebook details numerous transcriptome sequencing and analysis projects, often using tools like Trinity and DIAMOND for assembly and annotation. These studies investigate gene expression patterns in response to various factors, including environmental stress.
3 DNA Methylation Studies: The notebook documents several experiments investigating DNA methylation patterns in various species, employing techniques like bisulfite sequencing (BS-seq) and MethylMiner enrichment. These studies are often linked to understanding environmental responses and developmental processes.
4 Genotyping and SNP Analysis: The notebook details genotyping-by-sequencing (GBS) projects and the use of tools like Stacks and bcftools for variant calling and population genetics analyses, particularly in oysters.