ShoRAH

Short Reads Assembly into Haplotypes

Current version

0.5.1 January 2011

Description

ShoRAH is a software package that allows for inference about the structure of a population from a set of short sequence reads as obtained from ultra-deep sequencing of a mixed sample. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.

Download

ShoRAH is distributed under the GNU General Public License.

Download current version shorah-0.5.1 Jan 2011.

In addition to the computational improvements introduced in version 0.4, the current version includes a program to convert SAM alignments to a format readable for ShoRAH. We have also produced more documentation in the form of an online webpage. This now includes a detailed example on how to use ShoRAH with short reads

For changes between versions please see the file CHANGELOG.

Older versions

Links to previous versions are only for comparison reasons. We strongly recommend to use the most recent one.

• shorah-0.5 Aug 2010
• shorah-0.4 Jun 2010
• shorah-0.3.1 Feb 2010
• shorah-0.3 Jan 2010
• shorah-0.2 Oct 2008
• shorah-0.1 Jul 2008

Installation

ShoRAH has been tested under Linux and Mac OS X. With the distributed source code, it should also be possible to make it work under Windows. For instructions, please consult the INSTALL file or the online documentation.

Usage

Please refer to the README file. More detailed instructions are given in the online documentation.

Authors and Contributors

• Niko Beerenwinkel
• Arnab Bhattacharya
• Nicholas Eriksson
• Moritz Gerstung
• Lukas Geyrhofer
• Osvaldo Zagordi

Citations

• If you use the software ShoRAH please cite:
  Zagordi O, Bhattacharya A, Eriksson N, Beerenwinkel N (2011) ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. BMC Bioinformatics, vol. 12 p. 119
• The first paper where the method has been introduced and verified is:
  Eriksson N, Pachter L, Mitsuya Y, Rhee S-Y, Wang C, Gharizadeh B, Ronaghi M, Shafer RW, Beerenwinkel N (2008). Viral population estimation using pyrosequencing. PLoS Computational Biology, 4(5):e1000074.
• The improved error-correction method, based on Dirichlet process mixture, is described in:
  Zagordi O, Geyrhofer L, Roth V, Beerenwinkel N (2009). Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction. Journal of Computational Biology, 17:417-428.
• The verification of the improved error correction with experimental data is in:
  Zagordi O, Klein R, Däumer M, Beerenwinkel N (2010). Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies. Nucleic Acids Research, vol. 38 (21) pp. 7400-9

Contact

shorah@bsse.ethz.ch