Associated Scientists & Alumni

Facts & Details: 

Analysis tool to perform HLA calling with HiSeq2000/2500 and MiSeq data derived from targeted HLA enrichment (view publication).

Important to know:

  • the software was developed to analyze data that was generated like described in the publication
  • the main requirements for the algorithm are random fragmentation of the DNA, high coverage, entire gene coverage
  • it can be used for whole genome or exome data if you are an experienced HLAssign user, understood the algorithm (to make the correct decisions), have the entire gene covered for both alleles and perform manual calling for every locus
  • it can be used on long range PCR data (entire gene is covered), if random fragmentation was performed on the amplicons

Two versions of the analysis software are available. The console application, which is the first version of the HLA analysis algorithm. It is available as open source and must be compiled at the target system. It comes as it is and we do not support/update it any more. Feel free to change anything. The results of our publication (Nucl. Acids Res. (2015) doi: 10.1093/nar/gkv184 ) were calculated with this version. The second analysis software is HLAssign. Here we reimplement(ed) the algorithm and added a graphical user interface (GUI). It is available as Linux (64bit), Windows (64bit) and Mac OS X (64bit) executable. This software allows for easy data analysis and data screening. As it is still under development, please expect minor differences between the results of the GUI and the console application.


Reference data

Download the reference data set via SFTP:

server (SFTP): 
user         : HLAdata
password     : freehladata

The reference data set contains short read data (fastq) of all reference samples that were analyzed for the benchmark of our HLA typing method/analysis. Feel free to download all or only a couple of samples. The fastq folder contains two sub folders. The folder 100bp with all samples that were sequenced with read length 100 and the folder 98bp for those that have a read length of 98. For each sample there is a subdirectory with the sample identifier as the folder name.

Analysis software

Download (IMGT/HLA DB v3.21.0):

Ubuntu 14.04 64bit         Windows 7 64bit         Mac OS X

or pre-installed on a VirtualBox image, available through our SFTP resource (see above)

HLAssign tutorial

HLAssign GUI screenshot

Alternatively download the console application:

pilot project source code     bait design source code


We are working on an improved user interface. The initial design phases are finished and implementation runs in parallel with the further development of GUI v1.








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