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.
More information here.
The software suite ShoRAH (Short Reads Assembly into Haplotypes) consists of several programs, the most imporant of which are:
|Tool||What it does|
||wrapper for everything|
||amplicon based analysis|
||shotgun sequencing analysis|
||detects single nucleotide variants, taking strand bias into account|
||splitting shotgun sequencing .BAM into multiple overlapping windows|
||Gibbs sampling for error correction via Dirichlet process mixture|
||strand bias test|
If you use shorah, please cite the application note paper Zagordi et al. on BMC Bioinformatics.
ShoRAH and its dependencies are all available in bioconda. We strongly advise you to install this package for a hassle-free experience.
conda install shorah
shorah requires the following pieces of software:
Python 3 The required dependencies are:
a) Biopython, and b) NumPy. These packages can be downloaded using pip or conda
HTSlib which is used to access bam/cram/sam and fasta files.
zlib, which is used by HTSlib for compressing bam files
pkg-config, for discovering dependencies, which most Unix-like systems include
Boost C++ library, for random number generation
In addition, if you want to bootstrap the git version of shorah instead of using the provided tarballs, you will need the GNU Autotools:
m4, which most Unix-like system include
We strongly recommend you use one of the versioned tarballs from the releases page. ShoRAH uses Autoconf and Automake, and these tarballs include all necessary scripts and files required for installation, whereas the git tree only contains the bare minimum of files required for bootstrapping.
Further, we strongly recommend you use a virtualenv for python installation that shares the same directory
root as where you'd like to install shorah to. Not using a virtualenv means that the python dependencies will
not be located in the installation root, which will likely require you to specify
PYTHONPATH, making the
installation more brittle.
Say for instance, you would like to install shorah to
/usr/local/shorah. The first step consists of installing
the required python dependencies. Create a virtualenv:
/opt/local/bin/virtualenv-3.6 is the virtualenv command for python 3.6 on MacPorts. Now install
the python dependencies:
/usr/local/shorah/bin/pip install Biopython numpy
Now call the
configure script from the shorah tarball, taking care to specify the absolute path of the
python interpreter (or the relative one if it is in your
PATH), as this gets inserted into the shebang line of all python scripts:
./configure --prefix=/usr/local/shorah PYTHON=/usr/local/shorah/bin/python3.6
The configure script finds the dependencies using pkg-config. Once it completes, run:
4 specifies the number of compilation threads to use. Finally, after compilation, install using:
All the programs should now be located in
Boostrapping from git
If you opted to clone the git repository instead of downloading a prepared tarball, you will need to bootstrap the configure script:
autoreconf -vif -I m4
After this, you can run the
configure script as described previously.
For the developers who prefer this, it is alternatively possible to compile the C++ components with Meson and then install ShoRAH with pip in development mode using :
mkdir -p build cd build meson ../ ninja cd .. pip3 install -e .
Since Windows 10, Microsoft provides the Windows Subsystem for Linux which enables a linux environment under Windows.
The input is a sorted bam file. Analysis can be performed in local mode.
Note: Currently in ShoRAH2 global haplotype reconstruction is disabled. The last version of ShoRAH1 with global mode is v1.1.3 and can easily be obtained from bioconda. If you wish to perform global reconstruction, we suggest that you consider the global haplotype options available in V-pipe
The local analysis alone can be run invoking
shorah shotgun or
shorah amplicon (program
for the amplicon mode). They work by cutting window from the multiple sequence
diri_sampler on the windows and calling
shorah snv for the
SNV calling. See the
file in directory
file in directory
All changes to the C++ code in
src/cpp should always be formatted according to the included
.clang-format style by doing
clang-format -style=file -i src/cpp/*.[ch]pp
in the root of the repository.
You can also report your problems in the issue tracker on GitHub.