ShoRAH

Short Read Assembly into Haplotypes

Current version

0.2 October 2008

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.

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ShoRAH is distributed under the GNU General Public License.

• shorah-0.2 Oct 2008
• shorah-0.1 Jul 2008

For changes between versions please see the file CHANGELOG.

Installation

ShoRAH has been tested under Linux and Mac OS X.
Please consult the INSTALL file for instructions.

Known issues

It has ben reported that, on some architectures, the C++ code might fail to compile. Adding
#include <cstdlib> to both contain_src/contain.cc and freqEst_src/freqEst.cc at the top of the files should solve the issue (thanks for reporting this).

Line 193 of dec.py (del out_reads[mathc_rec.id]) should be commented out.

Next version of the software (summer 2009) will address these issues, and will contain several upgrades.

Authors and Contributors

Niko Beerenwinkel
Nicholas Eriksson
Lukas Geyrhofer
Osvaldo Zagordi

Citations

The general inference procedure is described in:

• Nicholas Eriksson, Lior Pachter, Yumi Mitsuya, Soo-Yon Rhee, Chunlin Wang, Baback Gharizadeh, Mostafa Ronaghi, Robert W. Shafer, Niko Beerenwinkel (2008)
  Viral population estimation using pyrosequencing
  PLoS Computational Biology, 4(5):e1000074
  paper online

The current implementation of the error correction step is not based on the k-means algorithm described in the PLoS paper. Rather, we use the Dirichlet process mixture for locally inferring haplotypes and correcting reads.

• Osvaldo Zagordi, Lukas Geyrhofer, Volker Roth, Niko Beerenwinkel
  Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction
  RECOMB 2009, LNCS 5541, pp. 345-358, 2009.

Contact

shorah@bsse.ethz.ch