DoubleCrossoversFasta

REDHORSE- A Software Suite to Detect Recombinations From Next-Generation Sequencing Data

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REDHORSE Package

Example Data

Find double crossovers

This utility finds double crossovers using multiple sequence alignment fasta file. Since it doesnt use the genomic positions, it is not accurate as the utility in REDHORSE that uses a merged allele file

Prerequisites

1) Multiple sequence alignment file that is generated using previous technologies.

How to run it?

REDHORSE takes the MSA as input and finds double crossovers using findDoubleCrossoversFASTA utility of REDHORSE as follows:

java -jar REDHORSE.jar findDoubleCrossoversFASTA -i fastaFile -o outputFileWithDoubleCrossovers -m parent1Name -n parent2Name -q numMarkersSupportingDoubleCrossoverRegion

-i is the MSA file
-o is the output file containing double crossovers
-m is name of the parent 1 in MSA file
-n is name of the parent 2 in MSA file
-q is the minimum number of markers supporting this doublecrossover region

Output

The output of the program is as follows:

sampleName Chromosome strt end numberofMarkers typeofSwitch
P1_29VBSF_GCTTAGA TGME49_chrVIIIorganism_Toxoplasma_gondii_ME49version_2012-08-28length_6970285 2716714 2717562 10 p1top2

sampleName is the name of the sample that had recombination, strt is the start position where double crossover started, end is the end position where double crossover ended, numberofMarkers is the number of markers supporting this region and typeofSwitch specifies if the hybrid switches from parent1 profile to parent2 profile or vice versa.

Index of Utilities
Analytical Pipeline