SEQscoring: a tool to facilitate the interpretation of data generated with next generation sequencing technologies

Authors

  • Katarina Truvé Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07 Uppsala
  • Oscar Eriksson Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07 Uppsala
  • Martin Norling Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07 Uppsala
  • Maria Wilbe Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Biomedical centre, Box 597, SE-751 24, Uppsala
  • Evan Mauceli Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), 7 Cambridge Center, Cambridge, Massachusetts, 02142
  • Kerstin Lindblad-Toh Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-751 23 Uppsala, Sweden; Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), 7 Cambridge Center, Cambridge, Massach (USA)
  • Erik Bongcam-Rudloff Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07 Uppsala

DOI:

https://doi.org/10.14806/ej.17.1.211

Keywords:

next generation sequencing, genome wide association study, candidate mutations

Abstract

Next Generation Sequencing (NGS) technologies promise a revolution in genetic research. Generating enormous amounts of data, they bring both new opportunities and new challenges to researchers. SEQscoring was designed to facilitate analysis and enable extraction of the most essential information from data produced in NGS resequencing projects. Its main functionality is to help researchers locate the most likely causative mutations for a specific trait or disease, but it can advantageously be used whenever the goal is to compare and explore haplotype patterns and to locate variations positioned in evolutionary conserved genomic elements. SEQscoring uses input data containing information about coverage and variations produced by other programs, like MAQ and SAMtools, and put the emphasis on methods for data visualisation and interpretation. We compare cases and controls in several ways and also utilise the power of comparative genomics, by scoring all variations according to their degree of conservation. The SEQscoring tool is publicly accessible via the Web. It has an intuitive interface and can easily be used by biologists, medical researchers, veterinarians as well as bioinformaticians. We exemplify how SEQscoring was used in a recent study as a subsequent step to a Genome Wide Association Studies (GWAS) to extract a set of candidate mutations.

Availability: http://www.seqscoring.org

Embnet.journal 17.1

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Published

2011-08-02

Issue

Vol. 17 No. 1: Next Generation Sequencing Data Analysis

Section

Research Papers

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