HeurAA: Accurate and Fast Detection of Genetic Variations with a Novel Heuristic Amplicon Aligner Program for Next Generation Sequencing

Lorinc S. Pongor, Ferenc Pintér, István Peták

Research output: Contribution to journalArticle

Abstract

Next generation sequencing (NGS) of PCR amplicons is a standard approach to detect genetic variations in personalized medicine such as cancer diagnostics. Computer programs used in the NGS community often miss insertions and deletions (indels) that constitute a large part of known human mutations. We have developed HeurAA, an open source, heuristic amplicon aligner program. We tested the program on simulated datasets as well as experimental data from multiplex sequencing of 40 amplicons in 12 oncogenes collected on a 454 Genome Sequencer from lung cancer cell lines. We found that HeurAA can accurately detect all indels, and is more than an order of magnitude faster than previous programs. HeurAA can compare reads and reference sequences up to several thousand base pairs in length, and it can evaluate data from complex mixtures containing reads of different gene-segments from different samples. HeurAA is written in C and Perl for Linux operating systems, the code and the documentation are available for research applications at http://sourceforge.net/projects/heuraa.

Original languageEnglish
Article numbere54294
JournalPloS one
Volume8
Issue number1
DOIs
Publication statusPublished - Jan 18 2013

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Fingerprint Dive into the research topics of 'HeurAA: Accurate and Fast Detection of Genetic Variations with a Novel Heuristic Amplicon Aligner Program for Next Generation Sequencing'. Together they form a unique fingerprint.

  • Cite this