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Ignacio Medina, 01/08/2013 05:52 pm



HPG Aligner is an ultrafast and highly sensitive Next-Generation Sequencing (NGS) read mapping. Many of current solutions for read mapping in NGS work well in a few scenarios, some work well for short reads but fail to map long reads, or viceversa, while others can map ungapped reads but no gapped reads, and others run very slow.

HPG Aligner has been designed to align short and long reads with high sensitivity, therefore any number of mismatches or indels are allowed. HPG Aligner implements to well known algorithms: Burows-Wheeler Transform (BWT) to speed-up mapping high-quality reads, and Smith-Waterman (SW) to increase sensitivity when reads cannot be mapped using BWT.

Both algorithms have been implemented taking advantage of new computing hardware such as multi-core CPUs, SIMD vectorized registers and GPUs, therefore a very high performance runtime is achieved with a low memory footprint.

HPG Aligner has been designed to work with three alignment modes:

  • dna: for DNA reads mapping
  • rna: RNA-seq mapping
  • bs (under development right now): BS-seq mapping

A fourth command build-index is available to build the indexes for BWT.


Main goals

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

This section will cover how to perform a basic NGS alignment.

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.