MHC Genotyping Pipeline v1.2


The MHC Genotyping Pipeline is an Mac OSX Application that performs MHC genotyping from Illumina MiSeq raw data. The MHC Genotyping Pipeline makes use of numerous open source software tools for the processing and analysis of sequencing reads. The executables, scripts, and package dependencies that comprise these tools are packaged within the OSX application file. Each individual packaged tool is released under it own license and terms and conditions. A complete list of packaged tools can be found below.

  • bbtools version 33.37b
  • pigz version 2.3.1
  • xlsxwriter version 0.7.2 - python module for writing excel files
  • bowtie-1.0.0
  • flash version 1.2.11
  • flexbar version 2.3.4
  • xlrd version 0.9.3 - python module for reading excel files

Installation Dependencies

The following needs to be installed prior to running the application:

  • MacOSX operating system version 10.6+ . Not tested on older versions.
  • python3, installed in /usr/local/bin/python3
  • Java Runtime environment 6
  • Java Runtime environment (latest)
  • Java JDK (latest)

Usage Instructions


The MHC genotyping pipeline accepts paired end Illumina MiSeq data in the form of gzipped fastq files. The pipeline expects amplicon sequencing data generated by PCR with MHC class I and II specific primers (see ____). The pipeline accepts either built in primer files and reference database files or user supplied files. The user specifies an output directory in which all temporary, reference and results files are stored during a run.

Major pipeline steps:
  • Decompression of reads
  • Sorting of reads by id (bbtools)
  • Trimming primers from reads (bbtools / flexbar)
  • Merging Reads (flash)
  • Mapping Reads (bowtie)
  • Parsing Mapping results
  • generate output files

Link to Complete MHC Genotyping Pipeline Documentation