ShoRAH

Short Reads Assembly into Haplotypes

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

Get the latest ShoRAH version at Github.

ShoRAH is distributed under the GNU General Public License.
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.

Documentation

Read the latest online documentation for help.

Data

Data sets are available here.

Authors and Contributors

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

Citations

Software:

• 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.

Methods and validation:

• 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.
• 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.
• 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

Archive

• shorah-0.6 Jul 2012
• shorah-0.5.1 Jan 2011
• 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