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This reference book compiles standard operating procedures, protocols, and applications of Next-Generation Sequencing (NGS). It discusses genomic testing applications through NGS and protocols for cataloging variants of uncertain significance.
List of contents
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
Index
About the author
Prashanth N Suravajhala is a Professor in the Systems Genomics Lab of the Department of Biosciences at Manipal University Jaipur. 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.
Summary
This reference book compiles standard operating procedures, protocols, and applications of Next-Generation Sequencing (NGS). It discusses genomic testing applications through NGS and protocols for cataloging variants of uncertain significance.
