ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data.
- Zagordi O Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland. osvaldo.zagordi@bsse.ethz.ch
- Bhattacharya A
- Eriksson N
- Beerenwinkel N
- 2011-04-28
Published in:
- BMC bioinformatics. - 2011
Genetic Variation
HIV
HIV Infections
High-Throughput Nucleotide Sequencing
Humans
Neoplasms
Sequence Analysis, DNA
Software
English
BACKGROUND
With next-generation sequencing technologies, experiments that were considered prohibitive only a few years ago are now possible. However, while these technologies have the ability to produce enormous volumes of data, the sequence reads are prone to error. This poses fundamental hurdles when genetic diversity is investigated.
RESULTS
We developed ShoRAH, a computational method for quantifying genetic diversity in a mixed sample and for identifying the individual clones in the population, while accounting for sequencing errors. The software was run on simulated data and on real data obtained in wet lab experiments to assess its reliability.
CONCLUSIONS
ShoRAH is implemented in C++, Python, and Perl and has been tested under Linux and Mac OS X. Source code is available under the GNU General Public License at http://www.cbg.ethz.ch/software/shorah.
With next-generation sequencing technologies, experiments that were considered prohibitive only a few years ago are now possible. However, while these technologies have the ability to produce enormous volumes of data, the sequence reads are prone to error. This poses fundamental hurdles when genetic diversity is investigated.
RESULTS
We developed ShoRAH, a computational method for quantifying genetic diversity in a mixed sample and for identifying the individual clones in the population, while accounting for sequencing errors. The software was run on simulated data and on real data obtained in wet lab experiments to assess its reliability.
CONCLUSIONS
ShoRAH is implemented in C++, Python, and Perl and has been tested under Linux and Mac OS X. Source code is available under the GNU General Public License at http://www.cbg.ethz.ch/software/shorah.
- Language
-
- English
- Open access status
- gold
- Identifiers
-
- DOI 10.1186/1471-2105-12-119
- PMID 21521499
- Persistent URL
- https://sonar.ch/global/documents/126884
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