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cbg-ethz / shorah

Repo for the software suite ShoRAH (Short Reads Assembly into Haplotypes)
GNU General Public License v3.0
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What is ShoRAH?

Build Status Bioconda package Docker container

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
shorah wrapper for everything
shorah amplicon amplicon based analysis
shorah shotgun shotgun sequencing analysis
shorah snv detects single nucleotide variants, taking strand bias into account
b2w splitting shotgun sequencing .BAM into multiple overlapping windows
diri_sampler Gibbs sampling for error correction via Dirichlet process mixture
fil strand bias test

Citation

If you use shorah, please cite the application note paper Zagordi et al. on BMC Bioinformatics.

General usage

Pre-built packages

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

Dependencies

shorah requires the following pieces of software:

  1. Python 3 The required dependencies are:

    a) Biopython, and b) NumPy. These packages can be downloaded using pip or conda

  2. HTSlib which is used to access bam/cram/sam and fasta files.

  3. zlib, which is used by HTSlib for compressing bam files

  4. pkg-config, for discovering dependencies, which most Unix-like systems include

  5. 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:

  1. Autoconf 2.69

  2. Automake 1.15

  3. m4, which most Unix-like system include

Installation

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 /usr/local/shorah

where /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:

make -j4

where 4 specifies the number of compilation threads to use. Finally, after compilation, install using:

make install

All the programs should now be located in /usr/local/shorah/bin.

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.

Meson

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 .

Windows users

Since Windows 10, Microsoft provides the Windows Subsystem for Linux which enables a linux environment under Windows.

Users of older versions of Windows can can install and run shorah with Cygwin. Please see the relevant paragraph on the documentation page.

Run

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

Local analysis

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 alignment, invoking diri_sampler on the windows and calling shorah snv for the SNV calling. See the README file in directory shotgun_test and the README file in directory amplicon_test.

Coding style

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.

All changes to the python code in src/shorah should always be formatted conforming to the PEP 8 style guide. To this end, we advise to use autopep8.

Contact

ShoRAH is maintained as part of the V-pipe virus NGS pipeline and you can easily reach out the developers on its website.

You can also report your problems in the issue tracker on GitHub.