Version 34 (Joaquin Tarraga, 01/09/2013 03:26 pm) → Version 35/56 (Ignacio Medina, 01/11/2013 11:40 am)


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h1. Introduction

h2. Overview

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.

h2. Goals

Main goals are:

* to develop a highly sensitive NGS read mapper, many of current solutions fail to map reads containing many mismatches, indels or introns
* to implement a High-Performance Computing (HPC) solution that performs very fast with a low memory footprint, to achieve this, we make use of multi-core CPUs, SIMD registers and GPUs
* to provide to the community with a open source solution where more people can contribute to the software development through a Gitorius server
* ...

h2. Main features

h1. Documentation

h2. 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.

h2. Tutorial

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

* [[tutorial|Tutorial]]
* [[cli|Command line interface (CLI) options]]

h2. Worked example

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

h1. Technical information

h2. Obtaining and building the software

h2. 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.

h3. Exome and genomic DNA mapping, _dna_ mode

h3. RNA-seq mapping, _rna_ mode

[[rna-seq_arch|RNA-seq architecture]]

h3. BS-seq

_Under development, it is scheduled for version 2_.

h2. Releases