Overview De novo sequencing refers to the sequencing and construction of a new genome or transcriptome. New sequences can provide novel insight into an organism’s biology and can also be used in comparative genomic studies. The process of mapping the reads from these projects is complicated because there is no reference sequence to which sequence […]
Brief summaries of the wide variety of applications that have been enabled by next generation sequencing. We include key technical characteristics that help match the applications with the best sequencing platforms.
Overview In addition to measuring levels of DNA and RNA in a cell, there are certain applications where it is important to know not just the level of particular sequences but also how these sequences are interacting with the proteome. These interactions can strongly influence the regulation of gene expression and are, therefore, critical for […]
Overview Metagenomics is the study of environmental samples where multiple microbial genomes are analyzed at the same time. It is in direct contrast to isolating and cultivating individual species prior to sequencing their genomes. The primary advantage of metagenomics is that it allows for the discovery and study of microbial genomes which would otherwise be […]
The methylation state of DNA (specifically that of the base cytosine) has been shown to influence the expression of genes. For example, in mammalian cells higher levels of methyl CpG around the transcription start site (TSS) have been associated with transcriptional silencing, although more complex patterns in other regions of the genome are being revealed. […]
Resequencing, especially with human samples, is one of the most popular applications of next-generation sequencing. It is used to determine the genomic variations of a sample in relation to a common reference sequence. The generated sequence is aligned to the reference sequence and mined for SNPs and CNVs as well as genomic rearrangements and indels. […]
Overview Targeted resequencing is a variation of re-sequencing where only a small subset of the genome is sequenced, such as the exome, a particular chromosome, a set of genes or a region of interest. Focusing on a subset of the genome is generally done to reduce costs, although there may be certain cases, such as […]
Overview Transcriptome sequencing encompasses a wide variety of applications from simple mRNA profiling to discovery and analysis of the entire transcriptome, including both coding mRNA and non-coding RNA (e.g., miRNA, small RNAs, linc RNAs). These applications, collectively called RNA-Seq, are extremely popular for next generation sequencing platforms as they uncover information that may be missed […]