SePIA statistics

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Citations per year

Citations chart

Popular tool citations

chevron_left Gene fusion detection Differential expression Bioinformatics workflows Read quality control SNV detection Read alignment Normalization Adapter trimming Known transcript quantification Bioinformatics workflows Spliced read alignment Variant detection chevron_right
Popular tools chart

Tool usage distribution map

Tool usage distribution map

Associated diseases

Associated diseases

SePIA specifications


Unique identifier OMICS_12000
Name SePIA
Alternative name Sequence Processing Integration and Analysis
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data The mandatory input files for SePIA’s first module are tab-delimited text files containing the following information: unique, per-sample IDs and the corresponding path to unprocessed .fq/.fastq file. Two optional columns can be added to provide further identification of ‘treatment’ and ‘sample’ information, which are required for differential analysis and visualization.
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Anduril, Docker
Source code URL
Maintained Yes


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  • person_outline Sampsa Hautaniemi <>

Publication for Sequence Processing Integration and Analysis

SePIA in publication

PMCID: 5802506
PMID: 29242506
DOI: 10.1038/s41408-017-0033-8

[…] phs000532.v2.p1), and the lymphoma/leukemia molecular profiling project (llmpp) (n = 233) (geo accession: gse10846) were used. cgci level 1 rna-seq data were downloaded and processed with sepia transcriptomics analysis pipeline. a web-based cutoff finder tool ( was used to determine the most prognostic cutoff level for survival outcomes. […]

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SePIA institution(s)
Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
SePIA funding source(s)
Supported by the Academy of Finland (Center of Excellence in Cancer Genetics Research), the Sigrid Jusélius Foundation, Finnish Cancer Associations, and Doctoral Programme in Biomedicine.

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