Next Generation Sequencing (NGS)/Epigenetics
Epigenetics is the science that studies inheritable traits not transmitted by plain sequence information. NGS can assess a particular non-standard epigenetics effect, which is the amount of methylation occurring on cytosines. This methylation is important biologically because it may influence the level of packing of chromatine and therefore affect efficiency of transcription in entire genomic areas. Cytosine methylation is reversible but inheritable somatically and germinally.
Genomic DNA can be treated with bisulfite, protocol that will transform only non-methylated cytosines into thymidines. Methylated cytosines are not affected, and will still be sequenced as such. A common NGS application in epigenetics is to align bisulfite-treated reads from a known organism on a reference genome, to assess the degree of methylation in particular areas. However, the complexity of the alignment will be higher, alongside with the reduced complexity of the reads (with several Cs being turned into Ts). Therefore, genomic DNA samples are sequenced both with and without bisulfite treatment, operation which allow to assess and normalize for the initial of reads aligning on specific regions.
Specific short read aligners exist for this task, just to name a few: