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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

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

start.txt · Last modified: 2016/05/03 08:37 by jpflorido

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