Illumina: Spotlight on the Companies Shaping Genetic Research

Established in 1998, Illumina began its journey into the field of genomics with the launch of its BeadArray technology for high-throughput genotyping of single nucleotide polymorphisms (SNPs). Through the key acquisition of sequencing company Solexa and the persistent development of their instruments, Illumina transformed itself into an international leader in sequencing technologies.

Illumina currently maintains a large majority of the sequencing market,...

Epigenetics research has played a valuable role in understanding different components of various diseases and disorders, and utilizing the proper tools and methods is vital. “The method of choice to analyze epigenetic modifications and their role in diseases is dependent on the epigenetics platform to be investigated,” explained Said Goueli, Senior Research Fellow at Promega. As reviewed in our recent articles, there are many important methods for epigenetic profiling. Using many...

In the first segment of our review of epigenetic sequencing methods, we covered methylation detection, chromatin accessibility, and protein-DNA interactions. This final part of our review will break outside of the standard analysis and cover some influential multidimensional methods.

Spatial Epigenomics
“Epigenetic assays, whether conducted at the single-cell or bulk level, have played a crucial role in unraveling the underlying mechanisms of diseases and...

Developments in sequencing technologies and methodologies have transformed the field of epigenetics, giving researchers a better way to understand the complex world of gene regulation and heritable modifications. This article explores some of the diverse sequencing methods employed in the study of epigenetics, ranging from classic techniques to cutting-edge innovations while providing a brief overview of their processes, applications, and advances.

Methylation Detect...

After covering QC and alignment tools in the first segment and variant analysis and genome assembly in the second segment, we’re wrapping up with a discussion about tools for differential gene expression analysis and data visualization. In this article, we include recommendations from the following experts: Dr. Mark Ziemann, Senior Lecturer in Biotechnology and Bioinformatics, Deakin University; Dr. Medhat Mahmoud Postdoctoral Research Fellow at Baylor College of Medicine;...

Continuing from our previous article, we share variant analysis and genome assembly tools recommended by our experts Dr. Medhat Mahmoud, Postdoctoral Research Fellow at Baylor College of Medicine, and Dr. Ming "Tommy" Tang, Director of Computational Biology at Immunitas and author of From Cell Line to Command Line.

Variant detection and analysis tools
Mahmoud classifies variant detection work into two main groups: short variants (<50...

With new tools and computational resources being released regularly, it can be hard to determine which are best suited for the analysis process and which older tools continue to be maintained. In an effort to assist the sequencing community, we interviewed three highly skilled bioinformaticians about their recommended tools for several important analysis applications.

Quality control and preprocessing tools
“Garbage in, garbage out” is a popular...

Variant Call Format (VCF) is an important file format that is specifically used for storing genetic variation data, such as single nucleotide polymorphisms (SNPs), small insertions or deletions (indels), and structural variations. These tab-delimited files contain useful information about the genomic location, reference allele, and alternate allele(s) for each variant. Due to their flexibility, VCF files are widely used in genomics research and are a key component in many genetic...

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Performing successful sequencing analysis requires an understanding of different file formats and how they are used for various applications. Scientists interested in completing their own sequencing analysis should learn the purpose and contents of each format. In the next two articles, we will explore some of the essential file formats used in sequencing data analysis and their significance in the field.

FASTA

The FASTA file format is one of the most...

As a continuation of our last article, we will be covering important metrics related to long-read sequencing technologies. In this article, we focus on metrics relevant to evaluating the success of a Pacific Biosciences (PacBio) sequencing run.

Pacific Biosciences

PacBio has become synonymous with their High Fidelity (HiFi) sequencing. Supported on their Sequel II and IIe instruments, and now expanded to their latest Revio sequencer, HiFi sequencing is built...