aRNApipe statistics

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Citations per year

Citations chart

Popular tool citations

chevron_left Gene fusion detection Read alignment Differential expression Bioinformatics workflows Read quality control Adapter trimming Alternative splicing events identification Known transcript quantification Spliced read alignment Variant detection chevron_right
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Tool usage distribution map

Tool usage distribution map

Associated diseases

Associated diseases

aRNApipe specifications


Unique identifier OMICS_12214
Name aRNApipe
Alternative name automated RNA-seq pipeline
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data An analysis configuration, and the samples to include in the analysis.
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Version 1.2
Stability Stable
Maintained Yes



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Publication for automated RNA-seq pipeline

aRNApipe in publication

PMCID: 5534072
PMID: 28754123
DOI: 10.1186/s13073-017-0458-5

[…] reads and a 6-bp index read, resulting in an average of 48.2 million reads per library. to quantify the expression of each gene in both pritzker and sncid datasets, rna-seq reads were processed with arnapipe v1.1 using default settings []. briefly, reads were aligned and counted with star v2.4.2a to all genes annotated in grch37_e75 []. all alignment quality metrics were obtained from the picard […]

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aRNApipe institution(s)
HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA; Rheumatology Research Group, Vall d'Hebron Hospital Research Institute, Barcelona, Spain; Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL, USA
aRNApipe funding source(s)
Supported by funds from The HudsonAlpha Institute for Biotechnology; by the NIH-National Institute of General Medical Sciences Medical Scientist Training Program (5T32GM008361-21); and by the William J. Maier III Fellowship in Cancer Prevention (Prevent Cancer Foundation).

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