REDHORSE-REcombination and Double crossover detection in Haploid Organisms using next-geneRation SEquencing data

BMC Genomics
Jahangheer S ShaikL David Sibley

Abstract

Next-generation sequencing technology provides a means to study genetic exchange at a higher resolution than was possible using earlier technologies. However, this improvement presents challenges as the alignments of next generation sequence data to a reference genome cannot be directly used as input to existing detection algorithms, which instead typically use multiple sequence alignments as input. We therefore designed a software suite called REDHORSE that uses genomic alignments, extracts genetic markers, and generates multiple sequence alignments that can be used as input to existing recombination detection algorithms. In addition, REDHORSE implements a custom recombination detection algorithm that makes use of sequence information and genomic positions to accurately detect crossovers. REDHORSE is a portable and platform independent suite that provides efficient analysis of genetic crosses based on Next-generation sequencing data. We demonstrated the utility of REDHORSE using simulated data and real Next-generation sequencing data. The simulated dataset mimicked recombination between two known haploid parental strains and allowed comparison of detected break points against known true break points to assess performance of re...Continue Reading

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Citations

Jul 1, 2016·Annual Review of Microbiology·Michael S BehnkeL David Sibley
Jul 23, 2015·BMC Genomics·Robert KingKim E Hammond-Kosack

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Methods Mentioned

BETA
three hybrids

Software Mentioned

wgsim
maxChi
CLC genomics workbench ( CLC Bio
3Seq
Java
GeneConv
Siscan
SAM
REDHORSE
SNV

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