Derivation of HLA class I and II predictions from shotgun sequence datasets

Project Description


HLAminer is a software for HLA predictions from next-generation shotgun (NGS) sequence read data and supports direct read alignment and targeted de novo assembly of sequence reads.


It has been used successfully to predict expressed HLA genes in the large TCGA (The Cancer Genome Atlas) cancer cohort. 

HLAminer uses TASR has its main assembly engine, which in turn is derived from SSAKE, the first de novo genome assembler published. A manuscript describing the methodology is published at Genome Medicine.


About the author: www.renewarren.ca


Targeted assembly: The HLA prediction by targeted assembly of short sequence reads performs targeted de novo assembly of HLA NGS reads and align them to reference HLA alleles from the IMGT/HLA sequence repository using commodity hardware with standard specifications (2GB RAM, 2GHz).

 Read alignment: The HLA prediction from direct read alignment method is conceptually simpler and faster to execute, since paired reads are aligned up-front to reference HLA alleles. However, the HLA allele detection sensitivity and specificity from this method is currently (100nt paired reads) lower than from targeted HLA assembly.

 *Alignments from both methods are processed by HLAminer to derive HLA class I and II predictions by scoring and evaluating the probability of each candidate allele bearing alignments.


If you use HLAminer in your research, please cite:


Warren RL, Choe G, Freeman DJ, Castellarin M, Munro S, Moore R, Holt RA.  2012. Derivation of HLA types from shotgun sequence datasets. Genome Med. 4:95.

Current Release
HLAminer 1.3.1

Released Oct 10, 2017

Streamlined output. Minor bug fixes.
More about this release…

Download file Get HLAminer for all platforms

All Releases

Version Released Description Compatibility Licenses Status
1.3.1 Oct 10, 2017 Streamlined output. Minor bug fixes. More about this release… BCCA (academic use) final
1.3 Sep 29, 2015 A more concise HLA allele summary and support for PacBio reads More about this release… BCCA (academic use) final
1.2 Feb 11, 2015 All HLA sequence databases have been updated Shell scripts that download HLA sequences corrected to reflect change of location at EBI (ie. fasta sub folder) Support added for predictions from direct alignment of single-end reads (-e option) More about this release… BCCA (academic use) final
1.1 Sep 16, 2014 Updated HLA databases, Streamlined code, Updated TASR dependency. Due to the clinical implications of HLAminer, the code is now released under the BC Cancer Agency Software License Agreement More about this release… BCCA (academic use) final
Project Resources

Project owner: Rene Warren