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.

Please cite

• Francisco J.López-Domingo, Javier P.Florido, Antonio Rueda, Joaquín Dopazo and Javier Santoyo-López (2014) ngsCAT: a tool to assess the efficiency of targeted enrichment sequencing, Bioinformatics, vol.30, no.12, pp.1767-1768, 2014; doi:10.1093/bioinformatics/btu108.

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