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Ryuto: Network-Flow based Transcriptome Reconstruction
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README.md

Overview

Ryuto is a tool for exact and fast transcript assembly and quantification, using network flows and a novel extension of splice-graphs.

Run

ryuto --help

to see options.

Testdata

You may download the alignments of real data used for publication here (Size: 82GB).

Pre-Compiled

Operation System Version Binary
Ubuntu 26 binary
Ubuntu 28 binary
Fedora 27 binary
Fedora 28 binary

Fedora users may have to install g++ in order for the pre-compiled binaries to work.

sudo dnf install gcc-c++

Installation

Download the newest source code from: https://github.com/studla/RYUTO

The following additional libraries need to installed in order to run Ryuto: zlib (openmp) boost htslib clp lemon

Compile Ryuto with:

./configure [options]
make

The compiled binary can then be found in the src subfolder.

ZLIB

htslib and thus Ryuto relies on zlib. If zlib is not installed on your system, you have to install it first. Download and install zlib from (https://zlib.net/).

Use the following commands to install zlib:

./configure
make
make install

Fedora users may alternatively run:

sudo dnf install zlib-devel

Ubuntu users may alternatively run:

sudo apt-get install zlib1g-dev

You may specify a non-standard zlib installation with --with-zlib=/path/to/your/zlib to the Ryuto ./configure call.

OpenMP

OpenMP is used for parallelization and needs to be installed in order for this feature to work.

Install Boost

Download and install boost from (http://www.boost.org).

On Fedora you may run:

sudo dnf install boost-devel

On Ubuntu you may run:

sudo apt-get install libboost-all-dev

If installed to a non-standard path, add with --with-boost=/path/to/your/boost to the Ryuto ./configure call.

Install htslib

Download and install htslib from (https://github.com/samtools/htslib). Install with:

./configure
make
make install

You may alternatively use the following call if bz2 is not installed.

./configure --disable-bz2 --disable-lzma

If installed to a non-standard path, add with --with-htslib=/path/to/your/htslib to the Ryuto ./configure call.

Install Clp

Download and install clp. Please use the version provided in the libraries_to_install subfolder. You may find details under (https://projects.coin-or.org/Clp).

Use the following call to install Clp to a custom location

./configure --disable-bzlib --disable-zlib --prefix=/path/to/your/clp
make
make install

If installed to a non-standard path, add with --with-clp=/path/to/your/clp to the Ryuto ./configure call..

Install Lemon

Download and install lemon after clp. Please use the version provided in the libraries_to_install subfolder. The provided version contains a simplified makefile. If you want to use your own version of lemon, please make sure it is linked appropriately to CBC, CLP and COIN-UTILS. You may find details under (http://lemon.cs.elte.hu/trac/lemon).

Install using

mkdir build
cd build
cmake -DLEMON_DEFAULT_LP=CLP -DCOIN_ROOT_DIR=/path/to/your/Clp ..
make
make install

If installed to a non-standard path, add with --with-lemon=/path/to/your/lemon to the Ryuto ./configure call.

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