HomeoRoq pipeline

HomeoRoq specifications


Unique identifier OMICS_21224
Name HomeoRoq
Alternative name Homeolog Ratio and Quantification
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Parental genomic sequences [Parent1_genome.fas] and [Parent2_genome.fas] and RNA-seq reads (paired-end), 6 libraries.
Input format FASTA
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Requirements STAR, Samtools, R-package locfit (used in “calcpval_one.R”), R-package doMC (used in “calcpval_one.R”)
Maintained Yes



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  • person_outline Jun Sese <>
  • person_outline Kentaro Shimizu <>
  • person_outline Satoru Akama <>

Publication for Homeolog Ratio and Quantification

HomeoRoq citation

PMCID: 5062318

[…] total levels of gene expression were estimated in the allopolyploids including both origin and common reads counted using htseq 0.5.4 in union mode after the read classification was bundled in the homeoroq pipeline as described in the following equation (1): rpkmx,i=109cx,igit, where x∈{lyr, hal} (1)chal,i=hi+ mi hihi+li clyr,i=li+milihi+li where cx,i is the number of reads that are mapped […]

HomeoRoq institution(s)
Department of Computer Science, Tokyo Institute of Technology, Tokyo, Japan; Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of Zurich, Zurich, Switzerland
HomeoRoq funding source(s)
Supported by Young Investigator Award of Human Frontier Science Program; Marie Heim-Vogtlin grant of the Swiss National Science Foundation (SNF) and Forschungskredit of University of Zurich; the University Research Priority Programs of Evolution in Action of the University of Zurich and of Systems Biology/Functional Genomics; JSPS KAKENHI [23128504, 24651227 and 24680032] and Grant-in-Aid for Scientific Research on Innovative Area "Genome Science", Ministry of Education, Culture, Sports, Science and Technology in Japan.

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