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Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

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Related Experiment Video

Updated: Dec 28, 2025

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Published on: April 11, 2016

Assembling and Validating Bioinformatic Pipelines for Next-Generation Sequencing Clinical Assays.

Jeffrey A SoRelle¹, Megan Wachsmann¹, Brandi L Cantarel^2,3,4

¹Department of Pathology (SoRelle, Wachsmann), University of Texas Southwestern Medical Center, Dallas.

Archives of Pathology & Laboratory Medicine

|February 12, 2020

Summary

This guide helps molecular pathologists implement bioinformatics pipelines for clinical next-generation sequencing (NGS) assays. It covers analysis design, validation, and resources for accurate genetic variation detection and interpretation.

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Last Updated: Dec 28, 2025

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

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Published on: April 11, 2016

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Published on: September 20, 2016

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

Area of Science:

Genomic Medicine
Bioinformatics
Clinical Laboratory Science

Background:

Clinical next-generation sequencing (NGS) adoption presents challenges in analyzing large datasets.
Bioinformatics pipelines are crucial for identifying genetic variations in clinical samples.
Accurate genetic alteration detection relies on algorithm choice, genome assembly, and annotation databases.

Purpose of the Study:

To provide a guide for molecular pathologists on bioinformatics analysis and validation design.
To assist in navigating regulatory and validation standards for clinical NGS bioinformatics pipelines.
To inform the implementation of new clinical NGS assays.

Main Methods:

Review of published studies on genomic analysis and bioinformatics.
Inclusion of methods comparison studies.
Identification of open-source software tools and databases for genetic variant detection.

Main Results:

Covers bioinformatic analysis design for genetic variation detection.
Details resources for assessing genetic effects.
Discusses validation experiments with diverse samples for accuracy and reproducibility.
Explores the role of proficiency testing in improving laboratory concordance.

Conclusions:

Bioinformatic pipeline design and validation are critical for clinical NGS.
Available resources support genetic variant detection and interpretation.
Proficiency testing may enhance consistency among clinical laboratories.