FindConventionalRecombinationsFasta

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

MAIN

INDEX

ANALYTICAL PIPELINE

CONTACT

SYSTEM REQUIREMENTS

REDHORSE Package

Example Data

Find Conventional Recombinations using multiple sequence alignments(MSA)

REDHORSE also finds recombinations using multiple sequence alignments. This utility therefore supports data from previous technologies

Prerequisites

1) MSA file generated using any previous method

How to run it?

REDHORSE takes the MSA file as input and finds conventional recombinations using findConventionalRecombinationsFASTA utility as follows:

java -jar REDHORSE.jar findConventionalRecombinationsFASTA -i MSAfastaFile -j OutputAllRecombinations -k OutputDirectoryIndividualRecombFiles -m parent1Name -n parent2Name

-i is multiple sequence alignment file
-j is the output file that contains locii where atleast one hybrid had a recombination
-k is the output directory where recombination information in each hybrid is reported individually
-m is the is name of the parent 1 in MSA file
-n is the is name of the parent 2 in MSA file

Output

The output1 (-j) of the program is as follows:
Chromosome Position ref alt s1 s2 s3 s4 s5
TGME49_chrVIIIorganism_Toxoplasma_gondii_ME49version_2012-08-28length_6970285 703053 A C A C A C C
TGME49_chrVIIIorganism_Toxoplasma_gondii_ME49version_2012-08-28length_6970285 1579995 C A C A C C A
ref is the allele from reference genome, alt is the alternate allele, s1-s5 are the allele composition of each sample and pos is the position where recombination occurred

Index of Utilities
Analytical Pipeline