Halvade statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Halvade

Tool usage distribution map

This map represents all the scientific publications referring to Halvade per scientific context
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Associated diseases


Popular tool citations

chevron_left Read alignment SNP detection SNV detection Variant detection chevron_right
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Halvade specifications


Unique identifier OMICS_08309
Name Halvade
Alternative name Halvade-RNA
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Input data Paired-end reads.
Input format FASTQ
Output data The single nucleotide variants (SNVs) and additionally insertions and deletions (indels) in certain pipelines.
Output format VCF
Operating system Unix/Linux
Programming languages Java
Parallelization MapReduce
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.2.1
Stability Stable
Source code URL https://codeload.github.com/biointec/halvade/tar.gz/1.2.1
High performance computing Yes
Maintained Yes
Wikipedia https://github.com/biointec/halvade/wiki




No version available



  • person_outline Jan Fostier

Additional information


Publications for Halvade

Halvade citations


Scalability and Validation of Big Data Bioinformatics Software

Comput Struct Biotechnol J
PMCID: 5537105
PMID: 28794828
DOI: 10.1016/j.csbj.2017.07.002

[…] e the underlying hardware and software resources. There have been many bioinformatics SaaS solutions to perform tasks ranging from short-read alignment (CloudAligner and SparkBWA ), variant calling (Halvade and Churchill ) and RNA-seq analysis (Oqtans and Falco ). In Platform as a Service, users are provided with a platform for developing their own software. Some PaaS providers also provide sup […]


elPrep: High Performance Preparation of Sequence Alignment/Map Files for Variant Calling

PLoS One
PMCID: 4504710
PMID: 26182406
DOI: 10.1371/journal.pone.0132868

[…] feature is interesting for connecting interactive applications to sequencing pipelines, but we need to further explore the impact on performance of our approach.elPrep can be used as a plugin for the Halvade MapReduce framework for executing sequencing pipelines in parallel on a cluster []. This is particularly interesting for further parallelising the execution of whole-genome data. […]

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Halvade institution(s)
Department of Information Technology, IDLab, Ghent University - imec, Ghent, Belgium; Janssen Research & Development, a division of Janssen Pharmaceutica N.V., Beerse, Belgium; Imec, Leuven, Belgium; Intel Corporation Belgium, Leuven, Belgium; ExaScience Life Lab, Leuven, Belgium
Halvade funding source(s)
Supported by Intel, Janssen Pharmaceutica, the Institute for the Promotion of Innovation through Science and Technology in Flanders (IWT): IWT O&O Projects 130405 and 130406.

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