1st Edition

Next-Generation Sequencing Standard Operating Procedures and Applications

Edited By Prashanth N Suravajhala, Jeff W Bizzaro Copyright 2025
    320 Pages 54 Color & 6 B/W Illustrations
    by CRC Press

    This cutting-edge reference book compiles standard operating procedures, protocols, and applications of Next-Generation Sequencing (NGS). It discusses genomic testing applications through NGS. It pays special focus on the protocols for cataloging variants of uncertain significance. Over the years, NGS and advanced bioinformatics approaches have allowed the transition of genomic assays into translational practices. The book covers visualization of NGS data sets, investigation of early development impairment, and metagenome protocols. It also discusses the challenges in NGS methods.

    Key Points-

    ·       Includes case studies of application of next-generation sequencing in different taxa like humans, rodents, plants, bacteria

    ·       Compiles protocols from various reputed companies like Illumina, PacBio, ThermoFisher

    ·       Discusses the translational applications of NGS methods

    ·       Reviews Machine Learning Heuristics For NGS data interpretation

    ·       Discusses emerging genomic assay technologies and characterizing mechanisms of disease prevalence

    The book is meant for researchers and industry experts in genomics, computational biology, and bioinformatics.

    1.     Technologies, Computations and Data Analysis  for Next Generation Sequencing

    2.     Epigenetics: RNA-Seq, ChiP-Seq, MedIP-Seq and ATAC-Seq

    3.     Streamlining Next-Generation Sequencing Data Analysis with Nextflow and nf-core Pipelines

    4.     Best practices for variant calling using Genome Analysis Toolkit

    5.     Implementation of WGCNA for identifying regulatory modules in biological networks

    6.     Meta-analysis of RNA-seq and Microarray data

    7.     Best practices in single-cell RNA-seq data analysis

    8.     Integration of Spatial Transcriptomics and Single Cell RNA-Seq

    9.     Metagenomics Analysis Pipelines for Microbiome Studies: QIIME and Mothur

    10.  Standard Operating Procedure and Applications in Single-Cell Transcriptomics

    11.  Benchmarking and Evaluation of de novo Assembly Tools for Prokaryotic Long Reads from Oxford Nanopore Technologies

    12.  Best Practices for Reproducible of Microbial Genomics Analysis

    13.  Single Cell RNA-Seq Analyses in the Era of Artificial Intelligence

    14.  Towards single-molecule protein sequencing

    15.  SOPs on Effective Galaxy Workflows

    16.  Motif prediction using ChIP-Seq data analysis using Galaxy

    17.  Developing a Whole Exome Consensus Variant Calling Pipeline to Infer Causal Pathogenic Variants



    Prashanth N Suravajhala is a Principal Scientist, Systems Biology at the Amrita School of Biotechnology, Kerala, India. He has a PhD in Systems Biology from Aalborg University, Denmark. His group has benchmarked pipelines and developed methods for systems genomic integration. He is an Associate Editor of Frontiers in Genetics/Systems Biology, Bio-Protocol, Biomolecules, and BMC Medical Genomics.

    Jeff W Bizzaro has been involved in the field of bioinformatics for more than 25 years and has made significant contributions to the development of bioinformatics software. He is a co-founder of Bioinformatics.org, a professional network that advocates for open science and provides various resources to students and professionals.