RepeatSoaker specifications

Unique identifier:
OMICS_14820
Interface:
Command line interface
Input data:
A list of genomic coordinates of low complexity regions.
Output data:
A file with reads overlapping low complexity regions at a given threshold filtered out, the filtering statistics.
Operating system:
Unix/Linux
Computer skills:
Advanced
Requirements:
Bedtools
Software type:
Package/Module
Restrictions to use:
None
Input format:
BED,BAM
Output format:
BAM
License:
GNU General Public License version 3.0
Stability:
Stable
Maintained:
Yes

versioning

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RepeatSoaker distribution

download

RepeatSoaker support

Documentation

Maintainers

  • Mikhail Dozmorov <>
  • Jonathan Wren <>

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Credits

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Publications

Institution(s)

Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA; Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Immunobiology and Cancer Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA; Reynolds Oklahoma Center on Aging, Donald W. Reynolds Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA

Funding source(s)

Supported by the National Institute of Arthritis and Musculoskeletal and Skin Diseases (a subaward from grant # P30 AR053483), by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences (a subaward from grant # P30GM103510), by the National Center for Advancing Translational Sciences (CTSA award No. UL1TR000058), by NIH/NIGMS (P30GM110766, P20GM103456, P20GM103636), by NIH/NIAMS (R01AR065953, P50AR060804), and by the National Science Foundation division of Advanced CyberInfrastructure # ACI-1345426.

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