REDHORSE specifications


Unique identifier OMICS_14747
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data Sorted alignments of “reads” to the genome, merged allele file
Input format SAM, BAM
Output data Multiple Sequence Alignments, recombinations
Output format MSA
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes




No version available


  • person_outline Jahangheer Shaik

Publication for REDHORSE

REDHORSE citations


QTL Mapping and CRISPR/Cas9 Editing to Identify a Drug Resistance Gene in Toxoplasma gondii

PMCID: 5608495
PMID: 28671645
DOI: 10.3791/55185

[…] ucleotide polymorphism (SNP) in the SNFr progeny, several computational based open source resources can be used to analyze the data. To create the genetic map for the ME49-FUDRr X VAND-SNFr cross the REDHORSE software suite was developed that uses WGS alignments of the parents and progeny to accurately detect the genomic positions of genetic crossovers. This mapping information can then be combin […]


NextGen sequencing reveals short double crossovers contribute disproportionately to genetic diversity in Toxoplasma gondii

BMC Genomics
PMCID: 4326188
PMID: 25532601
DOI: 10.1186/1471-2164-15-1168

[…] Similarity fraction: 0.8 and by using Global alignment. Since the ME49 genome is haploid, we extracted the alleles with frequency greater than or equal to 80% and having a minimum coverage of 5 using REDHORSE []. Loci that did not meet these criteria were tagged as missing data. SNPs between the parental lines were used to define the inheritance of alleles in the hybrids. We identified a total of […]

REDHORSE institution(s)
Department of Molecular Biology, Washington University School of Medicine, St Louis, MO, USA; Molecular Parasitology Unit, Laboratory for Parasitic Diseases, NIAID, NIH, Bethesda, MD, USA
REDHORSE funding source(s)
This work was supported by grants from the NIH (AI059176, AI036629 and AI29646).

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