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News
Short Reads Assembly into Haplotypes
0.5.1 January 2011
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.
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 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.
Please refer to the README file. More detailed instructions are given in the online documentation.
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