Requirements

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Requirements and setup

Hardware requirements

HiLive is compatible with all Illumina sequencers generating BCL files, including the popular HiSeq and MiSeq devices. Although these devices come with their own computers for run control and analysis, HiLive requires a separate high performance computer that is connected to the sequencer via a fast network connection (gigabit LAN or faster).

The HiSeq computer itself should be a powerful multicore machine, however the optimal specifications might depend on the intended use case. For HiSeq devices and large (e.g. full human) reference genomes, we recommend at least 32 cores and 256 GB RAM as well as an SSD drive for temporary data with at least 512 GB capacity. Significantly smaller machines might be suitable for MiSeq devices and smaller reference genomes. Distributed and cloud systems are currently not supported.

Software requirements

HiLive currently runs only on Linux systems. We developed and tested HiLive on Ubuntu 14.04, but other distributions should work as well.

The following software is required:

• C++ compiler supporting C++11 standard
• CMake (>= v2.8)
• Boost library (system, filesystem, program_options)
• zlib library
• lz4 library

Building from source

Check out the source code from the project website. Compile HiLive with default k-mer size (k=15):

cd [hilive-code]
mkdir build && cd build
cmake .. 
make

To compile HiLive with a different k-mer size than k=15 make the following adjustment (here: k=10):

cd [hilive-code]
mkdir build && cd build
cmake -DHiLive_K 10 ..
make

If you encounter problems during compilation (such as wrong paths), we recommend using the ccmake interface to obtain more control over the build process.

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