The versions given below have been tested with this software, and are known to work, but earlier versions may work perfectly well:
- ea-utils (fastq-mcf and fastq-join)
- BWA (version 0.7.5a-r405)
- samtools
- python2.7
- pip (already included in python version 2.7.9 and higher)
- gnumake
- git
- SRA Toolkit (version 2.3.5)
- curl
All of these packages will be installed by pip aimhii. They can be installed separately by running pip install -r requirements.txt, using the requirements.txt file included in the repository.
- biopython
- HTSeq
- matplotlib
- numpy
- pysam