HLAminer

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.

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.

Citation:
Genome Med. 2012 Dec 10;4(12):95.
Derivation of HLA types from shotgun sequence datasets.
Warren RL, Choe G, Freeman DJ, Castellarin M, Munro S, Moore R, Holt RA*.

BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada. *rholt@bcgsc.ca.