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Ignacio Medina, 01/08/2013 04:54 pm



HPG Aligner is an ultrafast and highly sensitive Next-Generation Sequencing read mapping. It has been designed to align short and long reads with a focus in sensitivity, therefore any number of mismatches or indels are allowed. HPG Aligner It has been implemented to take advantage of new computing hardware such as multi-core CPUs, SIMD vectorized registers and GPUs, therefore a very high performance is achieved with a low memory footprint.

HPG Aligner has been designed with three align modes: dna, rna and bs. A forth command is available to build the indexes for BWT.


Main features


Getting started

This sections cover how to obtain the binary and dependencies, information about how to build indexes is also provided. Running a first example is also explained.


To explore the general information, installation and command line interface (CLI) options you can visit:

Worked example

Technical information

Obtaining and building the software

Architecture and benchmarks results of different modes:

Detailed information about the architecture and benchmarks of different command modes. Although HPG Aligner pipeline is very similar between different modes, some differences exist. Some benchmarks results are presented.

Exome and genomic DNA mapping, dna mode

RNA-seq mapping, rna mode

RNA-seq architecture


Under development, it is scheduled for version 2.