Francisco J López-Domingo1, Javier P Florido1, Antonio Rueda1, Joaquín Dopazo2, Javier Santoyo-Lopez1. 1. Bioinformatics 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. 2. Bioinformatics 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, SpainBioinformatics 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, SpainBioinformatics 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.
Abstract
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.
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.
Authors: Ka Wai Leong; Fangyan Yu; Viktor A Adalsteinsson; Sarah Reed; Gregory Gydush; Ioannis Ladas; Jiang Li; Kelan G Tantisira; Gerassimos Mike Makrigiorgos Journal: Nucleic Acids Res Date: 2019-12-16 Impact factor: 16.971
Authors: Arinjay Banerjee; Jalees A Nasir; Patrick Budylowski; Lily Yip; Patryk Aftanas; Natasha Christie; Ayoob Ghalami; Kaushal Baid; Amogelang R Raphenya; Jeremy A Hirota; Matthew S Miller; Allison J McGeer; Mario Ostrowski; Robert A Kozak; Andrew G McArthur; Karen Mossman; Samira Mubareka Journal: Emerg Infect Dis Date: 2020-06-19 Impact factor: 6.883