The Composition Based Referencing platform: for DNA read mapping and genome plotting, indexing and linking.
Supported functionalities:
- mapper: for mapping long and short reads to DNA sequences
- plotter: for high resolution plots of two genomes
- indexer: creating an index of any sequence file
- linker: finding similarities between many genomes, for use in circos plots
Check out the wiki (https://github.com/swarris/ComBaR/wiki) for more examples.
It uses the pyPaSWAS framework for sequence alignment (https://github.com/swarris/pyPaSWAS)
Platforms supported:
- NVIDIA GPU using CUDA (compute capability 1.3 and higher)
- NVIDIA GPU using OpenCL
- Intel CPU using OpenCL
- Intel Xeon Phi accelerator using OpenCL
- Other systems supporting OpenCL (AMD, Intel GPUs, etc) should be able to run the software, but are untested.
In most cases it is enough to clone the repository: git clone https://github.com/swarris/ComBaR.git
After that, please install:
- pip (https://docs.python.org/2.7/installing/)
- numpy: sudo pip install numpy (or pip install --user numpy)
- BioPython: sudo pip install Biopython (or pip install --user Biopython)
- In some cases, the python development packages are required (Ubuntu: sudo apt-get install python-dev)
Making use of the CUDA version (also recommended when using the OpenCL version on a NVIDIA GPU):
- Download CUDA sdk: https://developer.nvidia.com/cuda-downloads
- sudo pip install pyCuda (http://mathema.tician.de/software/pycuda/)
Making use of the OpenCL version:
- check dependencies or downloads for your system. See this wiki for some great pointers: http://wiki.tiker.net/OpenCLHowTo
- sudo pip install pyOpenCL
Getting pyPaSWAS: pyPaSWAS is required as a module. Run in the following two commands in the ComBaR root folder: git submodule init git submodule update
The two input files are mandatory. Through the options the user can specify the file types of the input files (default: fasta), an output file and a log file. When requested, ComBaR will terminate if the output file already exists.
Run it by calling:
- python combar.py |options| file1 file2
Help file:
- python combar.py --help
By default, pypaswas will use the first CPU device. This can be changed by using:
- --device_type=[CPU|GPU]
- --platform_name=[Intel|NVIDIA]
- --framework=[opencl|CUDA]
- --device=[int]
For example, this will select the CPU: --device_type=CPU --platform_name=Intel --framework=opencl
This will select the second NVIDIA GPU: --device_type=GPU --platform_name=NVIDIA --framework=CUDA --device=1
Use a fastq-file:
- python combar.py reads.fastq genome.fa -1 fastq -o out.txt --loglevel=DEBUG
Create a genome plot:
- python combar.py genomeA.fa genomeB.fa -o out.csv --program=plotter
Table 1. Key command line options
| Option | Long version | Description |
|---|---|---|
| -h | --help | This help |
| -L | --logfile | Path to the log file |
| --loglevel | Specify the log level for log file output. Valid options are DEBUG, INFO, WARNING, ERROR and CRITICAL | |
| -o | --output | Path to the output file. Default ./output |
| -O | --overrideOutput | When output file exists, override it (T/F). Default T (true) |
| -1 | --filetype1 | File type of the first input file. See bioPython IO for available options. Default fasta |
| -2 | --filetype2 | File type of the second input file. See bioPython IO for available options. Default fasta |
| -G | Float value for the gap penalty. Default -5 | |
| -q | Float value for a mismatch. Default -3 | |
| -r | Float value for a match. Default 1 | |
| --any | Float value for an ambiguous nucleotide. Default 1 | |
| --other | Float value for an ambiguous nucleotide. Default 1 | |
| --device | Integer value indicating the device to use. Default 0 for the first device. | |
| -c | Option followed by the name of a configuration file. This option allows for short command line calls and administration of used settings. |
For questions, e-mail s.warris@gmail.com