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

Project Description

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


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

The HLAminer manuscript is the second-highest viewed Genome Medicine manuscript in the last 30 days, and the 24th most viewed since journal inception (Aug. 19th, 2014).

Highly accessed manuscript at Genome Medicine

It uses TASR has its main assembly engine, which in turn is derived from SSAKE, the first de novo genome assembler published.

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 1.0.6

Released Oct 18, 2013

Updated HLA CDS and genomic databases fixed a bug in alignment parsing module
More about this release…

Download file Get HLAminer for all platforms
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All Releases

Version Released Description Compatibility Licenses Status
1.0.6 Oct 18, 2013 Updated HLA CDS and genomic databases fixed a bug in alignment parsing module More about this release… GPL
1.0.5 Jun 01, 2012 initial release More about this release… GPL final
Project Resources

Project owner: Rene Warren