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Short Reads Assembly into Haplotypes


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.


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.


Read the latest online documentation for help.


Data sets are available here.

Authors and Contributors


Methods and validation:




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