Related Experiment Video
Updated: May 2, 2026
Author Spotlight: Cost-Effective Transcriptomic Drug Screening - Unlocking New Targets
Published on: February 23, 2024
ngsCAT: a tool to assess the efficiency of targeted enrichment sequencing
Francisco J López-Domingo1, Javier P Florido1, Antonio Rueda1
1Bioinformatics Department, Genomics and Bioinformatics Platform of Andalusia (GBPA), 41092 Seville, Computational Genomics Department, Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain and Functional Genomics Node (INB), Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain.
Motivation:
Targeted enrichment sequencing by next-generation sequencing is a common approach to interrogate specific loci or the whole exome in the human genome. The efficiency and the lack of bias in the enrichment process need to be assessed as a quality control step before performing downstream analysis of the sequence data. Tools that can report on the sensitivity, specificity, uniformity and other enrichment-specific features are needed.
Results:
We have implemented the next-generation sequencing data Capture Assessment Tool (ngsCAT), a tool that takes the information of the mapped reads and the coordinates of the targeted regions as input files, and generates a report with metrics and figures that allows the evaluation of the efficiency of the enrichment process. The tool can also take as input the information of two samples allowing the comparison of two different experiments.
Availability And Implementation:
Documentation and downloads for ngsCAT can be found at http://www.bioinfomgp.org/ngscat.
More Related Videos
13:24Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
Published on: April 11, 2016
09:06High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
Published on: October 5, 2018
