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MethPat specifications

Information


Unique identifier OMICS_20275
Name MethPat
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Whole genome bisulfite short read sequencing data (WGBS), or Reduced Representation Bisulfite Sequencing (RRBS), or Bisulfite Amplicon Sequencing.
Programming languages Python
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Stability Stable
Requirements
Bismark and its dependencies (bwa).
Maintained Yes

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Maintainers


  • person_outline Nicholas Wong <>
  • person_outline Bernard Pope <>
  • person_outline Alexander Dobrovic <>

Publications for MethPat

MethPat in publication

PMCID: 5627074
PMID: 28989734
DOI: 10.1098/rsos.170248

[…] all reads, all or nearly all of the fragments of dna in the bisulfite sequencing experiment must be hemimethylated in the same direction for hemimethylation to be detected. recently, tools such as methpat and mpfe have been developed to study methylation patterns rather the levels []. amplicon bisulfite sequencing enables high coverage sequence data to be generated for both strands of dna, […]

MethPat institution(s)
Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, Australia; Murdoch Childrens Research Institute, The Royal Children’s Hospital, Parkville, VIC, Australia; Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia. Victoria n Life Sciences Computation Initiative (VLSCI), The University of Melbourne, Parkville, VIC, Australia; Department of Computing and Information Systems, The University of Melbourne, Parkville, VIC, Australia; Department of Pathology, The University of Melbourne, Parkville, VIC, Australia; Centre for Personalised NanoMedicine, Australian Institute of Nanotechnology and Bioengineering, The University of Queensland, Brisbane, QLD, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia; Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; BioInfoRx Inc., Madison, WI, USA; BioResearch Software Consultants, Battle Ground, WA, USA; Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia; School of Cancer Medicine, La Trobe University, Bundoora, VIC , Australia; Present Address: Pacific Edge Biotechnology Ltd, Dunedin, Otago, New Zealand
MethPat funding source(s)
Supported, in part, by National Breast Cancer Foundation of Australia (NCBF) (grants CG-08-07, CG-10-04 and CG-12-07), the Cancer Council of Victoria, grants from the Victorian Cancer Agency, the Melbourne Melanoma Project funded by the Victorian Cancer Agency Translational Research program and established through support of the Victor Smorgon Charitable Fund, and the Victorian Government Operational and Infrastructure Support Grant.

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