PSI -- Pan-genome Seed Index

This is an implementation of the method introduced in:

Ghaffaari, A. & Marschall, T. Fully-sensitive seed finding in sequence graphs using a hybrid index Bioinformatics, 2019, 35, i81-i89

How to Install

Dependencies

Minimum requirements

PSI uses many features introduced in C++17. In order to work with it, you need a C++17 compliant compiler first. It has been tested with these compilers:

Compiler	Version
GCC	8.3, 9.2, 10.2.0, 12.2.0, 15
AppleClang	14.0.0, 16.0.1
Clang (LLVM)	22

Required dependencies

PSI library is a header-only library. However, it depends on a few external libraries to work. Both psikt seed finder and PSI library need the following libraries to be installed before building:

• Zlib
• BZip2
• Protobuf (tested with <= 3.21.12)
• OpenMP (for DiVerG's Kokkos host backend, enabled by -DDIVERG_ENABLE_OPENMP=ON)

On Ubuntu they can be installed by:

$ sudo apt install zlib1g-dev libbz2-dev libprotobuf-dev protobuf-compiler

GCC ships OpenMP support (libgomp), so it is already available there. With other toolchains you may need it explicitly; e.g. on macOS with LLVM/Clang: brew install libomp.

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NOTE There is a bug in Protobuf 3.20.x causing a linking issue while compiling in debug mode (i.e. when CMAKE_BUILD_TYPE matches Debug). Otherwise, in Release mode, it should be fine.

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Configuring the source code and/or building auxiliary tools requires:

• CMake >=3.25

Bundled dependencies

There are a few more dependencies that are bundled with PSI; i.e. PSI can install them for you. If you want PSI to do so, specify -DUSE_BUNDLED_ALL=on when running cmake (explained later). These dependencies are:

• SeqAn, version 2.4.0
• kseq++, version 1.1.2
• DiVerG, version 1.1.4 (bundles GUM and Kokkos)

PSI build script will skip those dependencies that are already installed on your system. Besides, installing each dependency can be individually enabled or disabled by setting -DUSE_BUNDLED_<library> to on or off respectively.

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NOTE If the bundled version of SeqAn did not work for any reason, install it manually. Make sure that seqan-2.pc configuration file has been installed too. On Debian-based operating systems, the easiest way to install SeqAn might be using the package manager:

$ sudo apt install libseqan2-dev

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Installation

To install PSI (recommended):

$ git clone https://github.com/cartoonist/psi.git
$ mkdir psi/build
$ cd psi/build
$ cmake -DCMAKE_BUILD_TYPE=Release -DDIVERG_ENABLE_OPENMP=ON -DUSE_BUNDLED_ALL=on ..
$ make
$ sudo make install

Use PSI

There are two ways to include PSI into your project:

As a git submodule

If you are using CMake, the library can be added to your project as a git submodule. Then, calling add_subdirectory(path/to/psi) in the corresponding CMakeLists.txt file exports psi::psi target. The exported target defines include directories, transitive dependencies, and compiler flags required for building the project.

TODO: As an external dependency

Install PSI as an external dependency. If you are using CMake, find_package will import the psi::psi target, which can be used to link your project.

If you are not using CMake, the same information can also be retrieved using pkg-config. Or just take a look at <INSTALL_PREFIX>/lib/pkgconfig/psi.pc.

Development

In order to build the tests or auxiliary tools, just turn on BUILD_TESTING or BUILD_PSI_AUX_TOOLS options when running cmake:

$ cmake -DCMAKE_BUILD_TYPE=Debug -DDIVERG_ENABLE_OPENMP=ON -DBUILD_TESTING=on -DBUILD_PSI_AUX_TOOLS=on ..