HPG Aligner statistics

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HPG Aligner specifications

Information


Unique identifier OMICS_05479
Name HPG Aligner
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data DNA sequences, RNA sequences
Input format FASTQ
Output data Mapped sequences
Output format SAM, BAM
Operating system Unix/Linux, Mac OS
Programming languages C
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0.1
Stability Stable
Requirements
git, gcc, scons, zlib, curl, xml, curses, gsl, check
Maintained Yes

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Maintainer


  • person_outline Joaquin Tarraga <>

Publication for HPG Aligner

HPG Aligner in publication

PMCID: 4833417
PMID: 26740642
DOI: 10.1093/dnares/dsv039

[…] to the acceleration of the current pipelines of sequencing data processing. this strategy, implemented in a program that makes use of different high-performance computing (hpc) technologies, hpg aligner, shows an excellent performance with both, short and long reads, with runtimes presenting only a linear dependence with the number of reads., most modern mappers rely on the bwt indexing […]


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HPG Aligner institution(s)
Department of Computational Genomics, Centro de Investigación Príncipe Felipe, Valencia, Spain; Functional Genomics Node, Instituto Nacional de Bioinformática, Valencia, Spain; Departamento de Informática, Universidad de Valencia, Valencia, Spain; Departamento de Ingeniería y Ciencia de Computadores, Universitat Jaume, Castellón de la Plana, Spain; Instituto de Investigación en Informática de Albacete, Universidad de Castilla-La Mancha, Albacete, Spain; Universitat Politècnica de València, Instituto de Instrumentación para Imagen Molecular, Valencia, Spain; Grupo de Investigación Biomédica de Imagen, La Fe Polytechnic University Hospital, Valencia, Spain; Bioinformatics of Rare Diseases, CIBER de Enfermedades Raras, Valencia, Spain
HPG Aligner funding source(s)
Funded by Spanish Ministry of Economy and Competitiveness), the HPC4G initiative and the Bull-CIPF Chair for Computational Genomics.

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