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Overview

ngsCAT (Next Generation Sequencing data Capture Assessment Tool) is a command-line application written in Python which facilitates a comprehensive evaluation of the performance of the capture step in targeted high-throughput sequencing experiments in terms of:

  • Sensitivity, which assesses the quality of the coverage on target regions. It is also important to provide a means of estimating how this coverage would improve by increasing sequencing depth.
  • Specificity, which measures how much of the sequencing effort is wasted on sequencing off-target bases.
  • Uniformity, which assesses sequencing biases due to specific genomic locations or nucleotide composition.

ngsCAT is an easy-to-use tool that can be run with just one command line in a standar computer, generating a detailed HTML report with metrics, summary tables, figures and plots that evaluate the efficiency of targeted enrichment sequencing.

Citation for ngsCAT

Please cite

if you find ngsCAT helpful and it has been used in your publication. Thank you.

start.txt · Last modified: 2016/05/03 10:37 by jpflorido

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