What is ShoRAH
ShoRAH is an open source project for the analysis of next generation sequencing data. It is designed to analyse genetically heterogeneous samples. Its tools are written in different programming languages and provide error correction, haplotype reconstruction and estimation of the frequency of the different genetic variants present in a mixed sample.
The software suite ShoRAH (Short Reads Assembly into Haplotypes) consists of several programs, the most imporant of which are:
amplian.py - amplicon based analysis
dec.py - local error correction based on diri_sampler
diri_sampler - Gibbs sampling for error correction via Dirichlet process mixture
contain - removal of redundant reads
mm.py - maximum matching haplotype construction
freqEst - EM algorithm for haplotype frequency
snv.py - detects single nucleotide variants, taking strand bias into account
shorah.py - wrapper for everything
If you use shorah, please cite the application note paper on BMC Bioinformatics.
Dependencies and installation
Please download and install:
- Biopython, following the online instructions.
- GNU scientific library GSL, installation is described in the included README and INSTALL files.
- ncurses is required by samtools. It is usually already included in Linux/Mac OS X.
Type ‘make’ to build the C++ programs. This should be enough in most cases. If your GSL installation is not standard, you might need to edit the relevant lines in the
/opt/local/ is already included).
Although we did not develop shorah for Windows, Cygwin offers a Linux-like environment on Windows machines. Users have reported successful compilation by installing Cygwin and then
Then, compile shorah with
make. We would like to hear if you succeed. Thanks to NKC
The input is a sorted bam file. Analysis can be performed in local or global mode.
The local analysis alone can be run invoking
amplian.py (program for the amplicon mode). They work by cutting windows from the multiple sequence alignment, invoking
diri_sampler on the windows and calling
snv.py for the SNV calling.
The whole global reconstruction consists of the following steps:
- error correction (i.e. local haplotype reconstruction);
- SNV calling;
- removal of redundant reads;
- global haplotype reconstruction;
- frequency estimation.
These can be run one after the other, or one can invoke
shorah.py, that runs the whole process from bam file to frequency estimation and SNV calling.
See the dedicated page.
Authors and Contributors