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. […]

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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