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ngsCAT: a tool to assess the efficiency of targeted enrichment sequencing

Francisco J. López-Domingo, Javier P. Florido, Antonio Rueda, Joaquín Dopazo, Javier Santoyo-Lopez
2014 Bioinformatics  
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.  ...  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  ...  This tool has been used as a quality control for 4600 exomes sequenced in our facility in the context of the Medical Genome Project (http://www.medicalgenomeproject.com), allowing us to detect samples  ... 
doi:10.1093/bioinformatics/btu108 pmid:24578402 fatcat:hcbgei7cbvclxlsm2ooe6g3qqu

A nuclease-polymerase chain reaction enables amplification of probes used for capture-based DNA target enrichment

2019 Nucleic Acids Research  
Here we provide a novel isothermal amplification reaction to amplify rapidly existing probe panels without knowledge of the sequences involved, thereby decreasing a major portion of the overall sample  ...  TBD-reactions generate enough capture-probes to increase by approximately two to three orders-of-magnitude the target-enrichment experiments possible from an initial set of probes.  ...  The authors declare that all data supporting the findings of this study are available within the paper and its Supplementary Data. SUPPLEMENTARY DATA Supplementary Data are available at NAR Online.  ... 
doi:10.1093/nar/gkz870 pmid:31598677 pmcid:PMC6902007 fatcat:oxobu2onzngmvee4dwjhr5v5ky

Effects of sample age on data quality from targeted sequencing of museum specimens: what are we capturing in time?

Angela McGaughran
2020 BMC Genomics  
When sequenced reads are aligned to a reference genome or to only the targeted region, older samples have a lower number of sequenced and mapped reads, lower mean coverage, and lower estimated library  ...  Sample age has significant, measurable impacts on the quality of NGS data following targeted enrichment.  ...  I would like to thank Rebecca Laver for completing the library preparation for many of the samples in this paper, and Terry Newman for providing statistical advice.  ... 
doi:10.1186/s12864-020-6594-0 pmid:32111157 pmcid:PMC7048091 fatcat:yixywd4uo5akjgafxrat45kxhy