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



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  • person_outline Jan Fostier <>

Additional information


Publications for Halvade

Halvade in publication

PMCID: 5537105
PMID: 28794828
DOI: 10.1016/j.csbj.2017.07.002

[…] 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 […]

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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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