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Version 15 (Ignacio Medina, 01/08/2013 04:54 pm) → Version 16/56 (Ignacio Medina, 01/08/2013 05:22 pm)


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h1. Introduction

h2. Overview

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 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</span> 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 runtime is achieved with a low memory footprint.

HPG Aligner has been designed to work</span> with three alignment align modes:

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

</span> dna, rna and bs. A fourth forth command _*build-index*_ is available to build the indexes for BWT. So,

</span>

h2. Goals

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

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