For Wrangling HLA Alleles
Python 2.7
Reads are self-aligned to create a consensus sequence.
This requires Anaconda to run.
Anaconda uses separate environments to run your programs in.
Install Anaconda for python 2.7.
https://www.continuum.io/downloads
To set up the environment in anaconda:
Linux/Mac:
conda create --name minionvironment biopython six pycurl pysam
source activate minionvironment
pip install pyinstaller packaging matplotlib
source deactivate
Windows:
conda create --name minionvironment biopython six pycurl pywin32 pysam
call activate minionvironment && pip install pyinstaller packaging matplotlib && call deactivate
You must also have clustalo installed for this program to generate initial consensus. 'clustalo' i used apt-get to install that on ubuntu. On Windows: http://www.clustal.org/omega/
It uses bw aligner for iterating the reads. Also used ubuntu to install that. 'bwa'
Future: can we split groups of reads for heterozygous alleles, and then assemble?
Future: Can we HLA allele call?