Deepak Kumar, PhD
Deepak Kumar, PhD Genomics Software Application Engineer

Deepak Kumar is a Genomics Software Application Engineer (Bioinformatics) at Agilent Technologies. He is the founder of the Expert Sequencing Program (ExSeq) at Cheeky Scientist. The ExSeq program provides a holistic understanding of the Next Generation Sequencing (NGS) field - its intricate concepts, and insights on sequenced data computational analyses. He holds diverse professional experience in Bioinformatics and computational biology and is always keen on formulating computational solutions to biological problems.

Articles Written By Deepak Kumar, PhD

Structural Variant Calling From NGS Data

By: Deepak Kumar, PhD

Single Nucleotide Variant (SNVs) have been considered as the main source of genetic variation, therefore precisely identifying these SNVs is a critical part of the Next Generation Sequencing (NGS) workflow. However, in this report from 2004, the authors identified another form of variants called the Structural Variants (SVs), which are genetic alterations of 50 or more base pairs, and result in duplications, deletions, insertions, inversions, and translocations in the genome. The changes in the DNA organization resulting from these SVs have been shown to be responsible for both phenotypic variation and a variety of pathological conditions. While the average variation,…

Essential Concepts in Gene Prediction and Annotation

By: Deepak Kumar, PhD

After genome assembly (covered in my previous blog) comes the vital step of gene prediction and annotation. This step entails the prediction of all the genes present in the assembled genome and to provide efficient functional annotation to these genes from the data available in diverse public repositories; such as Protein Family (PFAM), SuperFamily, Conserved Domain Database (CDD), TIGRFAM, PROSITE, CATH, SCOP, and other protein domain databases. It is imperative to understand that prediction and annotation of non-protein-coding genes, Untranslated Regions (UTR), and tRNA are as vital as protein-coding genes to determine the overall genetic constitution of the assembled genome. …

5 Essential Concepts In Genome Assembly From NGS data

By: Deepak Kumar, PhD

The main goal for researchers, clinicians, and students who perform Next Generation Sequencing (NGS) and produce sequenced data for diverse projects involving human samples is to find biomarkers or variants to make diagnoses; and deduce the genetic anomalies that could be responsible for the disease they are conducting research on. Most projects (academic or non-academic) constitute the prior ideology on deciphering the “unknown.” There are well-versed computational protocols and pipelines formulated by labs across the world in determining what the “unknown” variants are. The fact that we have the “reference” human genome available – thanks to the Human Genome Project – plays…

The Essential Dos and Don'ts of NGS (Next Generation Sequencing)

By: Deepak Kumar, PhD

Next Generation Sequencing (NGS) is a rapidly evolving and widely used method worldwide in both academic and non-academic settings. One of the most valuable aspects of NGS is producing millions of sequenced reads with diverse read lengths from small amounts of input DNA. NGS methods are extremely versatile; producing reads as short as 75 bp, as seen in SOLiD sequencing, to long reads ranging upwards of 1000bp in the case of Pyrosequencing.  Both long and short reads fill a unique niche for researchers. Longer reads generated from NGS are excellent for genomic rearrangement and genome assembly projects; especially when there…