ROP specifications

Information


Unique identifier OMICS_11866
Name ROP
Alternative name Read Origin Protocol
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.0
Stability Stable
Requirements
FASTQC, SEQLEAN, BLAST+, ncSplice, Bowtie2, CIRI, IgBLAST, MetaPhlAn, Samtools, Bamtools, HTSeq
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Noah Zaitlen

Publication for Read Origin Protocol

ROP citation

library_books

ROP: dumpster diving in RNA sequencing to find the source of 1 trillion reads across diverse adult human tissues

2018
Genome Biol
PMCID: 5857127
PMID: 29548336
DOI: 10.1186/s13059-018-1403-7

[…] pped reads can inform future development of read mapping methods, provide access to additional biological information, and resolve the irksome puzzle of the origin of unmapped reads. We developed the Read Origin Protocol (ROP), a multi-step approach that leverages accurate alignment methods for both host and microbial sequences. The ROP tool contains a combination of novel algorithms and existing […]

ROP institution(s)
Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA; Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA; Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; Department of Molecular and Computational Biology, University of Southern California, CA, USA; Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, and Cardiovascular Research Institute, University of California, San Francisco, CA, USA; Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA; Department of Medicine, University of California, San Francisco, CA, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA; Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA; Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University California Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA; Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, Netherlands; Pediatric Pulmonology, San Juan, Puerto Rico; Department of Pediatrics, National Jewish Health, Denver, CO, USA; University of Colorado School of Medicine, Denver CO, USA; Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel

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