{"id":29606588,"url":"https://github.com/bcgsc/hlaminer","last_synced_at":"2025-07-20T17:06:02.399Z","repository":{"id":21083037,"uuid":"24382839","full_name":"bcgsc/HLAminer","owner":"bcgsc","description":"⛏ HLA predictions from NGS shotgun data","archived":false,"fork":false,"pushed_at":"2025-04-14T17:46:44.000Z","size":174859,"stargazers_count":52,"open_issues_count":0,"forks_count":15,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-04-14T18:45:06.412Z","etag":null,"topics":["alignments","hla-prediction","hla-sequence","oxford-nanopore","shotgun-sequence-datasets","targeted-assemblies"],"latest_commit_sha":null,"homepage":"","language":"Perl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bcgsc.png","metadata":{"files":{"readme":"readme.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2014-09-23T17:52:26.000Z","updated_at":"2025-04-14T17:46:47.000Z","dependencies_parsed_at":"2025-04-14T18:41:22.352Z","dependency_job_id":null,"html_url":"https://github.com/bcgsc/HLAminer","commit_stats":{"total_commits":59,"total_committers":3,"mean_commits":"19.666666666666668","dds":0.03389830508474578,"last_synced_commit":"984a39f51034f11ffc6ea5165211e2161db726ee"},"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/bcgsc/HLAminer","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bcgsc%2FHLAminer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bcgsc%2FHLAminer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bcgsc%2FHLAminer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bcgsc%2FHLAminer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bcgsc","download_url":"https://codeload.github.com/bcgsc/HLAminer/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bcgsc%2FHLAminer/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266161904,"owners_count":23885928,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["alignments","hla-prediction","hla-sequence","oxford-nanopore","shotgun-sequence-datasets","targeted-assemblies"],"created_at":"2025-07-20T17:06:00.609Z","updated_at":"2025-07-20T17:06:02.392Z","avatar_url":"https://github.com/bcgsc.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Release](https://img.shields.io/github/release/warrenlr/HLAminer.svg)](https://github.com/warrenlr/HLAminer/releases)\n[![Downloads](https://img.shields.io/github/downloads/warrenlr/HLAminer/total?logo=github)](https://github.com/warrenlr/HLAminer/releases/download/v1.4/HLAminer_1-4.tar.gz)\n[![Issues](https://img.shields.io/github/issues/warrenlr/HLAminer.svg)](https://github.com/warrenlr/HLAminer/issues)\n[![link](https://img.shields.io/badge/HLAminer-manuscript-brightgreen)](https://doi.org/10.1186/gm396)\n[![link](https://img.shields.io/badge/HLAminer-protocol-brightgreen)](https://doi.org/10.1002/cpz1.70124)\nThank you for your [![Stars](https://img.shields.io/github/stars/warrenlr/HLAminer.svg)](https://github.com/warrenlr/HLAminer/stargazers)\n\n\n![Logo](https://github.com/warrenlr/hlaminer/blob/master/hlaminer-logo.png)\n\n## HLAminer (c) 2011-present\n\n\nDerivation of HLA (Human Leukocyte Antigen) class I and II predictions from DNA/RNA sequencing datasets\n\n*This manual assumes that you have a working knowledge of Unix, and some shell and perl scripting experience\n\n\n### CONTENTS\n--------\n1. [SYNOPSIS](#synopsis)\n2. [LICENSE](#license)\n3. [OVERVIEW](#overview)\n4. [DESCRIPTION](#description)\n5. [INSTALL](#install)\n6. [COMMANDS AND OPTIONS](#commands)\n7. [PREDICTING FROM LONG (NANOPORE/PACBIO) READS](#nanopore)\n8. [REFERENCE SEQUENCE FOR LONG-READ ALIGNMENTS](#reference)\n9. [DATABASES](#databases)\n10. [AUTHORS](#authors)\n11. [CITING](#citing)\n12. [FULL LICENSE](#full)\n--------\n### SYNOPSIS \u003ca name=synopsis\u003e\u003c/a\u003e\n--------\n\n  HLAminer is a pipeline for predicting Human Leukocyte Antigen (HLA) signatures from shotgun sequence data (ie. whole genome, whole transcriptome/RNA-Seq, exome), at the group and allele resolution.\n  It supports predictions from a variety of DNA sequencing technologies including those from Illumina, MGI, PacBio and Oxford Nanopore.   \n  Predictions are either derived from targeted sequence assembly, or direct sequence alignments.\n\n  For quick tests on Illumina RNA-seq data:\n  1. Copy ./test-demo/    eg. cp -rf test-demo foo\n  2. In folder \"foo\", edit the patient.fof file to point to your NGS RNAseq data.  Ensure all paths are ok.\n  3. For HLA Predictions by Targeted Assembly of Shotgun Reads: execute ./HLAminer/foo/HPTASRrnaseq.sh \n     For HLA Predictions by Read Alignment: execute ./HLAminer/foo/HPRArnaseq.sh\n\n\n### LICENSE \u003ca name=license\u003e\u003c/a\u003e\n--------\n\n  HLAminer Copyright (c) 2011-present Canada's Michael Smith Genome Science Centre.  All rights reserved.\n  TASR Copyright   (c) 2010-present Canada's Michael Smith Genome Science Centre.  All rights reserved.\n  SSAKE Copyright  (c) 2006-present Canada's Michael Smith Genome Science Centre.  All rights reserved.\n   \n  Due to the clinical implications of HLAminer, the code is now released\n  under the BC Cancer Agency software license agreement (academic use).\n  Details of the license can be accessed at:\n  and at the bottom of this readme file\n\n  For commercial licensing options, please contact Patrick Rebstein prebstein@bccancer.bc.ca\n\n  Software components of HLAminer (eg. TASR) are still distributed under the\n  terms of the GNU General Public License\n\n\n### OVERVIEW \u003ca name=overview\u003e\u003c/a\u003e\n--------\n\nDerivation of HLA class I and class II predictions from shotgun sequence datasets (HLAminer) by:\n1) Targeted Assembly of Shotgun Reads (HPTASR)\n2) Read Alignment (HPRA)\n\nBEST SHORT READ RESULTS ARE OBTAINED WITH HPTASR WITH READS 100bp AND UP (IDEALLY 150bp).\nIT WILL WORK WITH SHORTER READS (50bp) BUT 4-digit HLA ALLELE PREDICTIONS MAY BE AMBIGUOUS \n\nThis clip summarizes the pipeline:\nhttps://www.youtube.com/watch?v=j-g8Geh5ST8\u0026list=LL\u0026index=110\n\n\n### DESCRIPTION \u003ca name=description\u003e\u003c/a\u003e\n--------\n\nThe HLA prediction by targeted assembly of short sequence reads (HPTASR), performs targeted de novo assembly of HLA NGS reads and align the resulting contigs to reference HLA alleles from the IMGT/HLA sequence repository using commodity hardware with standard specifications (\u003c2GB RAM, 2GHz).  Putative HLA types are inferred by mining and scoring the contig alignments and an expect value is determined for each.  The method is accurate, simple and fast to execute and, for transcriptome data, requires low depth of coverage. Known HLA class I/class II reference sequences available from the IMGT/HLA public repository are read by TASR using default options (Warren and Holt 2011) to create a hash table of all possible 15 nt words (k-mers) from these reference sequences. Note that this parameter is customizable and larger k values will yield predictions with increased specificity (at the possible expense of sensitivity). Subsequently, NGS data sets are interrogated for the presence of one of these kmers (on either strand) at the 5’ or 3’ start. Whenever an HLA word is identified, the read is recruited as a candidate for de novo assembly. Upon de novo assembly of all recruited reads, a set of contigs is generated.  Only sequence contigs equal or larger than 200nt in length are considered for further analysis, as longer contigs better resolve HLA allelic variants.  Reciprocal BLASTN alignments are performed between the contigs and all HLA allelic reference sequences. HPTASR mines the alignments, scoring each possible HLA allele identified, computing and reporting an expect value (E-value) based on the chance of contigs characterizing given HLA alleles and, reciprocally, the chance of reference HLA alleles aligning best to certain assembled contig sequences\n\nThe HLA prediction from direct read alignment (HPRA) method is conceptually simpler and faster to execute, since paired reads are aligned up-front to reference HLA alleles.  Alignments from the HPTASR and HPRA methods are processed by the same software (HLAminer.pl) to derive HLA-I predictions by scoring and evaluating the probability of each candidate bearing alignments.\n\n\n### What's new in version 1.4?\n--------\n\nAbility to stream the (.sam) output of modern read  aligners, directly into HLAminer.\nInitial support for predicting HLA types from long nanopore reads such as those from Oxford Nanopore Technologies.\nBetter information/sub-routine/date tracking in hlaminer \n\n\n### What's new in version 1.3?\n--------\n\nA more concise HLA allele summary in HLAminer_HPTASR.csv and HLAminer_HPRA.csv (associated .log is unchanged and lists all predictions)\nKeeps top two [highest-scoring by HLA group] predictions per gene and only the 'P' designated allele when the summary include HLA Sequences reported to have the same antigen binding domain.\nFor the original output, refer to the HLAminer_v1-2.pl included in the ./bin directory\nA prediction example from MCF-7 PacBio RNA-seq reads is also provided\n\n\n### What's new in version 1.2?\n--------\n\nUpdated all HLA sequence databases\nCorrected shell script that download HLA sequences to reflect change of location at EBI (ie. fasta sub folder) \nAdded support for predictions from direct alignment of single-end reads\n\n\n### INSTALL \u003ca name=install\u003e\u003c/a\u003e\n--------\n\u003cpre\u003e\n1. Download and decompress the tar ball\ngunzip HLAminer_v1-4.tar.gz \ntar -xvf HLAminer_v1-4.tar\n2. Make sure you see the following directories:\n./bin\n./databases\n./docs\n./test-demo\n\n3. Read the docs in the ./docs/ folder\n4. Change/Add/Adjust the perl shebang line of each .pl and .sh script in the ./bin/ folder as needed\n\u003c/pre\u003e\nFrom direct Read Alignment (HPRA, faster but less accurate):\nHPRArnaseq_classI.sh\nHPRArnaseq_classI-II.sh\nHPRAwgs_classI.sh\nHPRAwgs_classI-II.sh\n-and for single end reads-\nHPRArnaseq_classI_SE.sh\nHPRArnaseq_classI-II_SE.sh\nHPRAwgs_classI_SE.sh\nHPRAwgs_classI-II_SE.sh\n\n\nFrom Targeted Assembly (HPTASR, longer but more accurate):\nHPTASRrnaseq_classI.sh\nHPTASRrnaseq_classI-II.sh\nHPTASRwgs_classI.sh\nHPTASRwgs_classI-II.sh\n\n*Running HPTASRwgs(rnaseq)_classI-II.sh will take longer than HPTASRwgs(rnaseq)_classI.sh, due to the reciprocal BLAST step.  You may remove this step from the former (and HLAminer.pl command) to speed things up.  However, this step is helpful in weeding out spurious alignments to HLA references.  That said, if you're solely interested in HLA-I, you have the option to run the latter set of scripts [HPTASRwgs(rnaseq)_classI.sh].\n\nAlso, in the ncbiBlastConfig2-2-XX.txt files (bin and test-demo directories), you may adjust the number of threads and number of reported alignments to speed things up. The options have different name depending on the blast version, refer to the blast manual\neg.\nv2.2.22\noption:description\n-a:threads\n-v:number of descriptions\n-b:number of alignments\n\nv2.2.28\n-num_threads:threads\n-max_target_seqs:number of hit sequences to report (when output is 5/xml)\n\nIn our hands, a few tests show that blast 2.2.22 may be faster than blast+ (2.2.28) while\nproducing accurate results - HLAminer (Warren et al. 2012) was thoroughly tested with 2.2.22\n\nNCBI blast may be downloaded from:\nftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/\n-or-\nftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/\n\n\nHLAminer.pl\nparseXMLblast.pl\n[![link](https://img.shields.io/badge/TASR-github-yellow)](https://github.com/warrenlr/TASR)\n\n5. You must install perl module Bio::SearchIO to use HPTASR\n6. Edit the fullpath location of bwa and other software dependencies in the shell scripts in the ./bin/ folder, as needed\n7. For your convenience, ncbi blastall and formatdb have been placed in the ./bin/ folder and executed from the following shell scripts:\n\nNAME,PROCESS,NGS DATA TYPE,PREDICTIONS\nHPRArnaseq_classI.sh,Paired read alignment,RNAseq (transcriptome),HLA-I A,B,C genes\nHPRArnaseq_classI-II.sh,Paired read alignment,RNAseq (transcriptome),HLA-I A,B,C and HLA-II DP,DQ,DR genes\n\nHPRAwgs_classI.sh,Paired read alignment,Exon capture (exome) and WGS (genome),HLA-I A,B,C genes\nHPRAwgs_classI-II.sh,Paired read alignment,Exon capture (exome) and WGS (genome),HLA-I A,B,C and HLA-II DP,DQ,DR genes\n\nHPTASRrnaseq_classI.sh,Targeted assembly of sequence reads,RNAseq (transcriptome),HLA-I A,B,C genes\nHPTASRrnaseq_classI-II.sh,Targeted assembly of sequence reads,RNAseq (transcriptome),HLA-I A,B,C and HLA-II DP,DQ,DR genes\n\nHPTASRwgs_classI.sh,Targeted assembly of sequence reads,Exon capture (exome) and WGS (genome),HLA-I A,B,C genes\nHPTASRwgs_classI-II.sh,Targeted assembly of sequence reads,Exon capture (exome) and WGS (genome),HLA-I A,B,C and HLA-II DP,DQ,DR genes\n\nRun those scripts by specifying the relative path ../bin/blastall or ../bin/formatdb in the shell scripts AND config file \"ncbiBlastConfig.txt\".  Make sure HPRA and HPTASR are running in same-level directories to ../bin/ (eg. ../test-demo/)\n\n8. Before running on your data, inspect the ./test-demo/ folder and familiarize yourself with the files and the execution.  \n9. When you are ready and the demo works well, place the fullpath location of your short read fastq or fasta files in the \"patient.fof\" file.\n10. Make sure that the following files are in your working directory:\n\npatient.fof\nncbiBlastConfig.txt (specific to the version of blast you are using, see in\n../bin and ../test-demo directories\n\n### ADDITIONAL INSTALL NOTES ON MAC OSX\n\n#### install bioperl\n---------------\nsudo perl -MCPAN -e shell\ninstall CJFIELDS/BioPerl-1.6.923.tar.gz\nchange shebang line in all PERL (.pl) scripts and location of bioperl on your system in HLAminer.pl\n\n#### install ncbi blast\n------------------\ndownload and install blast-2.2.22-universal-macosx.tar.gz\nchange path to blast in ncbiconfig.txt\n\n#### install homebrew\n----------------\n\u003cpre\u003e\nruby -e \"$(curl -fsSL\nhttps://raw.githubusercontent.com/Homebrew/install/master/install)\"\n\nSince databases were indexed with older\nversion, had to re-index:\nbwa index -a is HLA_ABC_CDS.fasta\n\u003c/pre\u003e\n\nchange path to bwa in HPRA* shell scripts\n\nTEST YOUR INSTALL BY RUNNING THE SCRIPT IN test-demo. CONSULT THE README-FIRST.txt FILE\n\n\n### COMMANDS AND OPTIONS \u003ca name=commands\u003e\u003c/a\u003e\n--------\n\n\u003cpre\u003e\n\nUsage: ../bin/HLAminer.pl [v1.4]\nDerivation of HLA class I and II predictions from shotgun sequence datasets\n--------------------------------------------------------------------\nHPTASR (HLA Predictions by Targeted Assembly of Shotgun Reads):\n-b blastn alignments.........................\u003ctig_vs_hla-ncbi.coord\u003e\n-r reciprocal blastn.........................\u003chla_vs_tig-ncbi.coord\u003e\n-c contig fasta file.........................\u003cTASRhla200.contigs\u003e\n-z minimum contig size.......................\u003c200\u003e\n------------------------------- OR ---------------------------------\nHPRA (HLA Predictions by Read Alignment):\n-a sam alignments............................\u003c -a ngs_vs_hla.sam \u003e or \u003c -a stream \u003e\n-e single-end reads used (1=yes/0=no)........\u003c0\u003e\n--------------------------------------------------------------------\n-h hla fasta file............................\u003cHLA_ABC_CDS.fasta\u003e\n-p P-designation file........................\u003chla_nom_p.txt\u003e\n-i minimum % sequence identity...............\u003c99\u003e\n-q minimum log10 (phred-like) expect value...\u003c30\u003e\n-s minimum score.............................\u003c1000\u003e\n-n consider null alleles (1=yes/0=no)........\u003c0\u003e\n-l label (run name) -optional-\n\n\nThe shell scripts are set to filter out short (\u003c200) contigs that could blur HPTASR predictions.  Feel free to adjust as you see fit.\n\nLikewise, HLAminer.pl runs with the set defaults:\n-z minimum contig size.......................\u003c200\u003e (HPTASR)\n-i minimum % sequence identity...............\u003c99\u003e  (HPTASR / HPRA)\n-q minimum log10 (phred-like) expect value...\u003c30\u003e  (HPTASR / HPRA)\n-s minimum score.............................\u003c1000\u003e (HPTASR / HPRA)\n-n consider null alleles (1=yes/0=no)........\u003c0\u003e (HPTASR / HPRA)\n\u003c/pre\u003e\n\nThe minimum sequence identity applies to the short read paired alignment or blast alignment, depending on the choice made.  HLA predictions with a phred-like expect value lower than -q or a score lower than -s will not be diplayed.  Because IMGT/HLA reports numerous null alleles, an option exist to consider or not these unexpressed alleles. \n\nLikewise, TASR-based (Targeted Assembly of Short Reads) predictions could be\nimproved by using larger k values for assembly (-k). Experimentation for\nchoosing the ideal k to use depends on the input read length and is warranted. \n\n\n### PREDICTING FROM LONG (NANOPORE/PACBIO) READS \u003ca name=nanopore\u003e\u003c/a\u003e\n--------\n\nHLAminer v1.4 provides initial support for HLA prediction from raw uncorrected shotgun nanopore long reads (such as those from Oxford Nanopore Technologies).\nHLAminer v1.4 implements a streaming approach to reading .sam alignment files, supporting the alignment of GB worth of read data in a few hours and predictions within seconds of alignment completion, without saving costly .sam files to disk.\n\n*More information here:* \nWarren RL, Birol I. 2025. Streaming long-read sequence alignments for HLA\npredictions using HLAminer. Current Protocols. https://doi.org/10.1002/cpz1.70124\n\nWe tested the software on the NA19240 WGS promethion dataset (2018, older chemistry).\nhttps://gigabaseorgigabyte.wordpress.com/2018/05/24/promethion-human-genome-na19240/\nwith data available from ENA at this location:\nhttps://www.ebi.ac.uk/ena/data/view/PRJEB26791\n\n1) First, we downloaded read files (ERR2585112 and ERR2585115 from the ENA)\n\u003cpre\u003e\nnohup wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR258/005/ERR2585115/ERR2585115.fastq.gz \u0026\nnohup wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR258/002/ERR2585112/ERR2585112.fastq.gz \u0026\n\u003c/pre\u003e\n2) Then, we predicted HLA by running minimap2 and HLAminer v1.4:\n\u003cpre\u003e\n/usr/bin/time -v -o minimap_hlaminerERR2585115-1mod.time minimap2 -t 60 -ax map-ont --MD ../database/GCA_000001405.15_GRCh38_genomic.chr-only-noChr6-HLA-I_II_GEN.fa.gz ERR2585115.fastq.gz | ./HLAminer.pl -h ../database/HLA-I_II_GEN.fasta -s 500 -q 1 -i 1 -p ../database/hla_nom_p.txt -a stream\n\n-or-\n\n/usr/bin/time -v -o minimap_hlaminerERR2585115-2mod.time minimap2 -t 60 -ax map-ont --MD ../database/GCA_000001405.15_GRCh38_genomic.chr-only-chr6hlamasked-HLA-I_II_GEN.fa.gz ERR2585115.fastq.gz | ./HLAminer.pl -h ../database/HLA-I_II_GEN.fasta -s 500 -q 1 -i 1 -p ../database/hla_nom_p.txt -a stream\n\n\u003c/pre\u003e\nA test is provided at ./test-demo/HPRAwgs_ONTclassI-IIdemo.sh\n\nThe output files:\nHLAminer_HPRA_ERR2585115.csv\n-and-\nHLAminer_HPRA_ERR2585115.log\n\nyou generate should be comparable* to:\nHLAminer_HPRA_ERR2585115_test.csv\n-and-\nHLAminer_HPRA_ERR2585115_test.log\n\n*exact scores are not to be expected, because they vary based on the HLA sequence database used, which differ from different release of the code (and your own updating of HLA sequence databases, which is highly recommended to do before you use HLAminer).\n\nResults below demonstrate HLAminer's ability to fairly accurately predict HLA-I and -II types from direct [and streamed] nanopore sequencing reads [old chemistry] alignments \n\u003cpre\u003e\n\nHLAminer PREDICTIONS (top 2 per HLA allele group, by high-score):\n--------------------\n\nA*30:106/A*68:02P\nB*35:01P/B*57:01P ex. B*57:03P\nC*04:01P/C*18:01P\nF*01:01P\nG*01:01P\n\nDQA1*01:02P/DQA1*05:01P\nDQB1*05:02P/DQB1*03:03P ex. DQB1*03:01P\nDRB1*12:01P/DRB1*16:02P\nDPA1*02:02P/DPA1*01:03P\nDPB1*90:01P/DPB1*01:01P\nDRA*01:01P\n\n\n\nREPORTED TYPES (extracted from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5804087/#MOESM1 Supp file 1 13059_2018_1388_MOESM1_ESM.xlsx Tab S6, NA19240 (Child)):\n--------------\n \nA*30:01:01G/A*68:02:01G\nB*35:01:01G/B*57:03:01G\nC*04:01:01G/C*18:01:01G\nF*01:01:01:08;F*01:01:01:09;F*01:02;F*01:01:01:10;F*01:03:01:01;F*01:01:01:11;F*01:03:01:02;F*01:01:01:12;F*01:01:02:01;F*01:01:02:02;F*01:01:02:03;F*01:01:02:04;F*01:01:02:05;F*01:01:02:06;F*01:01:01:01;F*01:01:01:02;F*01:01:01:03;F*01:01:01:04;F*01:01:01:05;F*01:01:01:06;F*01:01:01:07/F*01:01:01:08;F*01:01:01:09;F*01:02;F*01:01:01:10;F*01:03:01:01;F*01:01:01:11;F*01:03:01:02;F*01:01:01:12;F*01:01:02:01;F*01:01:02:02;F*01:01:02:03;F*01:01:02:04;F*01:01:02:05;F*01:01:02:06;F*01:01:01:01;F*01:01:01:02;F*01:01:01:03;F*01:01:01:04;F*01:01:01:05;F*01:01:01:06;F*01:01:01:07 \nG*01:06;G*01:01:02:01;G*01:01:02:02;G*01:18;G*01:08:01;G*01:01:18;G*01:01:19/G*01:05N\nH*02:05/H*02:05         \nJ*02:01;J*01:01:01:05;J*01:01:01:04;J*01:01:01:03;J*01:01:01:02;J*01:01:01:01/J*02:01;J*01:01:01:05;J*01:01:01:04;J*01:01:01:03;J*01:01:01:02;J*01:01:01:01     L*01:01:02;L*01:01:01:01;L*01:01:01:02;L*01:01:01:03/L*01:02\n\nDQA1*01:02:01G/DQA1*05:01:01G\nDQB1*05:02:01G/DQB1*03:01:01G\nDRB1*12:01:01G/DRB1*16:02:01G\nDPA1*02:01:01G/DPA1*02:02:02G\nDPB1*01:01:01G/DPB1*01:01:01G\nDOA*01:01:05/DOA*01:01:02:03;DOA*01:01:02:02;DOA*01:01:02:01;DOA*01:01:04:02;DOA*01:01:04:01    DMA*01:01:01:02;DMA*01:01:01:01;DMA*01:04;DMA*01:03;DMA*01:02;DMA*01:01:01:04;DMA*01:01:01:03/DMA*01:01:01:02;DMA*01:01:01:01;DMA*01:04;DMA*01:03;DMA*01:02;DMA*01:01:01:04;DMA*01:01:01:03\nDMB*01:02;DMB*01:01:01:04;DMB*01:01:01:03;DMB*01:01:01:02;DMB*01:03:01:04;DMB*01:01:01:01;DMB*01:03:01:03;DMB*01:03:01:02;DMB*01:03:01:01;DMB*01:05;DMB*01:04/DMB*01:02;DMB*01:01:01:04;DMB*01:01:01:03;DMB*01:01:01:02;DMB*01:03:01:04;DMB*01:01:01:01;DMB*01:03:01:03;DMB*01:03:01:02;DMB*01:03:01:01;DMB*01:05;DMB*01:04\nDRA*01:01:01:01;DRA*01:02:01;DRA*01:01:01:02;DRA*01:02:02;DRA*01:01:01:03;DRA*01:02:03;DRA*01:01:02/DRA*01:01:01:01;DRA*01:02:01;DRA*01:01:01:02;DRA*01:02:02;DRA*01:01:01:03;DRA*01:02:03;DRA*01:01:02\n\u003c/pre\u003e\n\nFor more information, please refer to:\n[![link](https://img.shields.io/badge/HLAminer-preprint-brightgreen)](https://doi.org/10.48550/arXiv.2209.09155)\n[![link](https://img.shields.io/badge/HLAminer-protocol-brightgreen)](https://doi.org/10.1002/cpz1.70124)\n\n\n### REFERENCE SEQUENCE FOR LONG-READ ALIGNMENTS \u003ca name=reference\u003e\u003c/a\u003e\n--------\n#### Use of HG38 reference for long-read alignments with HLAminer\n\nHere’s why we originally used HG38 without chr6 for alignments with long reads:\n\n✅ 1. Excluding chr6 and replacing with complete HLA alleles improves allele resolution\nThe classical HLA loci (HLA-A, -B, -C, -DRB1, etc.) on chr6 are highly polymorphic and not well-represented in a linear reference.\nMapping short or long reads to the limited HLA representation in GRCh38 often results in ambiguous or incorrect alignment, especially for novel or rare alleles.\nBy using all known HLA alleles (from IPD-IMGT/HLA) in a dedicated contig, you're allowing your mapper (e.g. minimap2) to consider each allele as an independent path — effectively emulating a graph reference without the overhead.\n\n✅ 2. Keeping the rest of GRCh38 intact ensures genomic compatibility\nMost reads outside of the MHC region still align correctly to the standard GRCh38 chromosomes.\n\u003cpre\u003e\nGCA_000001405.15_GRCh38_genomic.chr-only-noChr6-HLA-I_II_GEN.fa.gz\n\u003c/pre\u003e\n\n\nImprovements to the reference sequence used with long-read alignments (April 2025):\n\n✅ 1. Masking of chr6 HLA locus (HG38 coordinates 28510120-33480577). This range is the standard extended (Class I, II, and III regions and flanking genes+regulatory regions relevant to immune function) MHC region definition from 1000 Genomes and GRC and it's masked in many genomics pipelines to improve mapping accuracy and downstream interpretation. https://www.ncbi.nlm.nih.gov/grc/human/regions/MHC?asm=GRCh38\n\u003cpre\u003e\nGCA_000001405.15_GRCh38_genomic.chr-only-chr6hlamasked-HLA-I_II_GEN.fa.gz\n\u003c/pre\u003e\n\n\nNotes:\n\u003cpre\u003e\n-Custom references are better suited to HLA inference than any static genome, including hs38DH, and the approach aligns with best practices in immunogenomics.\n-It's crucial for you to keep the HLA allele set up-to-date, and update+document+date those files frequently (see the database folder README and the DATABASES section below for details):\n\u003c/pre\u003e\n\u003cpre\u003e\nGCA_000001405.15_GRCh38_genomic.chr-only-noChr6-HLA-I_II_GEN.fa.gz\nGCA_000001405.15_GRCh38_genomic.chr-only-chr6hlamasked-HLA-I_II_GEN.fa.gz\n\u003c/pre\u003e\n\n### DATABASES \u003ca name=databases\u003e\u003c/a\u003e\n--------\n\nFollow these instructions to download updated HLA sequences from ebi/imgt (shell scripts to automatically download and format the databases exist in ./database/) and refer to README.txt in the ./database directory:\n\n\n1) Coding HLA sequences\n\nHLA CDS sequences from:\n\u003cpre\u003e\nwget ftp://ftp.ebi.ac.uk/pub/databases/imgt/mhc/hla/fasta/A_nuc.fasta\nwget ftp://ftp.ebi.ac.uk/pub/databases/imgt/mhc/hla/fasta/B_nuc.fasta\nwget ftp://ftp.ebi.ac.uk/pub/databases/imgt/mhc/hla/fasta/C_nuc.fasta\ncat A_nuc.fasta B_nuc.fasta C_nuc.fasta | perl -ne 'chomp;if(/\\\u003e\\S+\\s+(\\S+)/){print \"\u003e$1\\n\";}else{print \"$_\\n\";}' \u003e HLA_ABC_CDS.fasta\n../bin/formatdb -p F -i HLA_ABC_CDS.fasta\n/home/pubseq/BioSw/bwa/bwa-0.5.9/bwa index -a is HLA_ABC_CDS.fasta\n\u003c/pre\u003e\n\n2) HLA genomic sequences \n\nTo make the HLA genomic sequence database, execute these unix commands:\n\u003cpre\u003e\nwget ftp://ftp.ebi.ac.uk/pub/databases/imgt/mhc/hla/fasta/A_gen.fasta\nwget ftp://ftp.ebi.ac.uk/pub/databases/imgt/mhc/hla/fasta/B_gen.fasta\nwget ftp://ftp.ebi.ac.uk/pub/databases/imgt/mhc/hla/fasta/C_gen.fasta\ncat A_gen.fasta B_gen.fasta C_gen.fasta | perl -ne 'chomp;if(/\\\u003e\\S+\\s+(\\S+)/){print \"\u003e$1\\n\";}else{print \"$_\\n\";}' \u003e HLA_ABC_GEN.fasta\n../bin/formatdb -p F -i HLA_ABC_GEN.fasta\n/home/pubseq/BioSw/bwa/bwa-0.5.9/bwa index -a is HLA_ABC_GEN.fasta\n\u003c/pre\u003e\n\nFOR YOUR CONVENIENCE, A SINGLE SHELL SCRIPT CAN BE RUN FROM ../database TO\nUPDATE ALL IMGT-HLA SEQUENCE DATABASES AND CREATE BWA/BLAST INDEXES. JUST KEEP\nIN MIND THAT THIS IS DONE WITH A SPECIFIC VERSION OF THESE TOOLS, IF YOU\nUPGRADE, YOU WILL HAVE TO REGENERATE THE INDEXES\n******************************\n***../database/updateAll.sh***\n******************************\n\nNote: For alignment of nanopore genomic/transcriptomic reads, we recommend aligning to a file comprised of human genome chromosomes and HLA-I and -II alleles to reduce the noise in alignments (especially when running minimap2). If you are predicting from direct ONT (nanopore) or PacBio long read alignments, please update the genome files (refer to the above section \"Use of HG38 reference for long-read alignments with HLAminer\"):\n\nGenome file (without Chromosome 6):\n\u003cpre\u003e\nhttps://www.bcgsc.ca/downloads/btl/hlaminer/GCA_000001405.15_GRCh38_genomic.chr-only-noChr6.fa.gz\n\u003c/pre\u003e\nthen:\n\u003cpre\u003e\ncd database\ncat GCA_000001405.15_GRCh38_genomic.chr-only-noChr6.fa HLA-I_II_GEN.fasta | pigz - \u003e GCA_000001405.15_GRCh38_genomic.chr-only-noChr6-HLA-I_II_GEN.fa.gz\ncat GCA_000001405.15_GRCh38_genomic.chr-only-noChr6.fa HLA-I_II_CDS.fasta | pigz - \u003e GCA_000001405.15_GRCh38_genomic.chr-only-noChr6-HLA-I_II_CDS.fa.gz\n\u003c/pre\u003e\n\nGenome file (without HLA region on Chromosome 6):\n\u003cpre\u003e\nhttps://www.bcgsc.ca/downloads/btl/hlaminer/GCA_000001405.15_GRCh38_genomic.chr-only-chr6hlamasked.fa.gz\n\u003c/pre\u003e\nthen:\n\u003cpre\u003e\ncd database\ncat GCA_000001405.15_GRCh38_genomic.chr-only-chr6hlamasked.fa HLA-I_II_GEN.fasta | pigz - \u003e GCA_000001405.15_GRCh38_genomic.chr-only-chr6hlamasked-HLA-I_II_GEN.fa.gz\ncat GCA_000001405.15_GRCh38_genomic.chr-only-chr6hlamasked.fa HLA-I_II_CDS.fasta | pigz - \u003e GCA_000001405.15_GRCh38_genomic.chr-only-chr6hlamasked-HLA-I_II_CDS.fa.gz\n\u003c/pre\u003e\n\nor download those files (JAN/APR 2025 update) directly from:\nhttps://www.bcgsc.ca/downloads/btl/hlaminer/\n\n\n3) P designation files\n\nUpgrade the P designation info from:\n\ninfo:\nhttp://hla.alleles.org/wmda/index.html\n\nfile:\nhttp://hla.alleles.org/wmda/hla_nom_p.txt\n\n\n### OUTPUT FILES \u003ca name=\"OUTPUT\"\u003e\u003c/a\u003e\n--------\n\nHLA predictions from read pair alignments:\n\u003cpre\u003e\nHLAminer_HPRA.log\nHLAminer_HPRA.csv\n\u003c/pre\u003e\nHLA predictions from targeted assemblies:\n\u003cpre\u003e\nHLAminer_HPTASR.log\nHLAminer_HPTASR.csv\n\u003c/pre\u003e\nThe .log file tracks the process of HLA mining. It contains the following information:\n-HLAminer command and parameters utilized\n-Contig/read pair alignment output and best HLA hit for each\n-Initial gene summary, score and expect value\n-Final summary, listing all predictions by highest score (more likely).\n\nThe .csv file contains HLAminer predictions.  Predictions are listed by HLA\ngene and ranked by highest score.  Predictions 1) and 2) are expected to\nrepresent the two alleles for each.\n\neg.\n\u003cpre\u003e\n----------------------------------------------------------------------\nSUMMARY\nMOST LIKELY HLA-I ALLELES (Confidence (-10 * log10(Eval)) \u003e= 30, Score \u003e= 500)\nAllele,Score,Expect (Eval) value,Confidence (-10 * log10(Eval))\n----------------------------------------------------------------------\n\nHLA-A\nPrediction #1 - A*26\n        A*26:33,4179,5.22e-124,1232.8\n\nPrediction #2 - A*33\n        A*33:24,1791,2.41e-75,746.2\n\nPrediction #3 - A*68\n        A*68:05,597,1.85e-10,97.3\n\u003c/pre\u003e\n\nFrom these predictions, the individual is expected to be heterozygous with HLA-I A alleles A*26 and\nA*33. The chance, expect value and confidence are different representations of the same\nmetric. The Confidence represents the Expect value - Eval - as a score in a\nmanner analoguous to the phred score employed in sequencing to quickly assess\nthe likelihood of a base being correct. \n\nPredictions/read pair are ambiguous when there are multiple predicted allele groups and/or protein coding alleles with the same score.\n\n\n### AUTHORS \u003ca name=authors\u003e\u003c/a\u003e\n--------\n\n\u003cpre\u003e\nRene Warren\n\u003c/pre\u003e\n\n### CITING \u003ca name=citing\u003e\u003c/a\u003e\n--------\n\nThank you for your [![Stars](https://img.shields.io/github/stars/warrenlr/HLAminer.svg)](https://github.com/warrenlr/HLAminer/stargazers) and for using, developing and promoting this free software!\n\nIf you use HLAminer for you research, please cite:\n\n\u003cpre\u003e\nWarren RL, Choe G, Freeman DJ, Castellarin M, Munro S, Moore R, Holt RA. (2012)\nDerivation of HLA types from shotgun sequence datasets\nGenome Med. 4, 95. https://doi.org/10.1186/gm396\n\u003c/pre\u003e\n[![link](https://img.shields.io/badge/HLAminer-manuscript-brightgreen)](https://doi.org/10.1186/gm396)\n\nand\n\n\u003cpre\u003e\nWarren RL, Birol I. (2025)\nStreaming long-read sequence alignments for HLA predictions using HLAminer\nCurrent Protocols. 5, e70124. https://doi.org/10.1002/cpz1.70124\n\u003c/pre\u003e\n[![link](https://img.shields.io/badge/HLAminer-protocol-brightgreen)](https://doi.org/10.1002/cpz1.70124)\n\n\n### LICENSE AGREEMENT \u003ca name=full\u003e\u003c/a\u003e\n-----------------------------------------------------------\nBC CANCER AGENCY SOFTWARE LICENSE AGREEMENT (ACADEMIC USE)\n\nCAREFULLY READ THE FOLLOWING TERMS AND CONDITIONS. This License\nAgreement (the \"Agreement\") is a legal contract between you, your\nemployer, educational institution or organization (collectively, \"You\")\nand the British Columbia Cancer Agency (\"BCCA\") with respect to the\nlicense of the software, including all associated documentation\n(collectively, the \"Product\").\n\nBCCA is willing to license the Product to You only if You accept the\nterms and conditions of this Agreement. By clicking on the \"I ACCEPT\"\nbutton, or by copying, downloading, accessing or otherwise using the\nProduct, You automatically agree to be bound by the terms of this\nAgreement. IF YOU DO NOT WISH TO BE BOUND BY THE TERMS OF THIS\nAGREEMENT, DO NOT COPY, DOWNLOAD, ACCESS OR OTHERWISE USE THE\nPRODUCT.\n\n1. AUTHORITY: In the event that You are an educational institution or\norganization, Your representative who is clicking the \"I ACCEPT\"\nbutton, or otherwise copying, downloading, accessing or using the\nProduct hereby, in their personal capacity, represents and warrants\nthat they possess the legal authority to enter into this Agreement\non Your behalf and to bind You to the terms of this Agreement.\n\n2. LICENSE TO USE: BCCA hereby grants to You a personal, non-exclusive,\nnon-transferable, limited license to use the Product solely for\ninternal, non-commercial use for non-profit research or educational\npurposes only on the terms and conditions contained in this Agreement.\nThe Product may be installed at a single site at Your premises only. A\ncopy of the Product installed on a single common machine or cluster of\nmachines may be shared for internal use by Qualified Users only. In\norder to be a \"Qualified User\", an individual must be a student,\nresearcher, professor, instructor or staff member of a non-profit\neducational institution or organization who uses the Product solely for\nnon-profit research or educational purposes.\n\n3. RESTRICTIONS: You acknowledge and agree that You shall not, and\nshall not authorize any third party to:\n(a) make copies of the Product, except as provided in Section 2 and\nexcept for a single backup copy, and any such copy together with the\noriginal must be kept in Your possession or control;\n(b) modify, adapt, decompile, disassemble, translate into another\ncomputer language, create derivative works of, or otherwise reverse\nengineer the Product, or disclose any trade secrets relating to the\nProduct, except as permitted in Section 5;\n(c) license, sublicense, distribute, sell, lease, transfer, assign,\ntrade, rent or publish the Product or any part thereof and/or copies\nthereof, to any third party;\n(d) use the Product to process any data other than Your own;\n(e) use the Product or any part thereof for any commercial or\nfor-profit purpose or any other purpose other than as permitted in\nSection 2; or\n(f) use, without its express permission, the name of BCCA.\n\n4. INTELLECTUAL PROPERTY RIGHTS: Subject to Section 5 below, all\npatents, copyrights, trade secrets, service marks, trademarks and\nother proprietary rights in or related to the Product and any\nimprovements, modifications and enhancements thereof are and will\nremain the exclusive property of BCCA or its licensors. You agree\nthat You will not, either during or after the termination of this\nAgreement, contest or challenge the title to or the intellectual\nproperty rights of BCCA or its licensors in the Product or any\nportion thereof.\n\n5. OWNERSHIP OF IMPROVEMENTS: In the event that the Product, in the\nform provided to You, includes source code (the \"Source Code\"),\nYou are entitled to make improvements, modifications and\nenhancements to the Source Code (collectively, \"Improvements\")\nwhich Improvements are to be used by You for non-profit research\nand educational purposes only and You shall be the owner of those\nImprovements that You directly make and of all intellectual\nproperty rights to such Improvements, subject to the foregoing\nlimits on Your use and distribution of such Improvements. You\nhereby grant to BCCA a perpetual, non-exclusive, worldwide,\nfully-paid, irrevocable license to use such Improvements for any\npurposes whatsoever, and to sublicense such Improvements including\nthe right for third parties to sublicense the same, in perpetuity\nto the extent such rights are not limited in duration under\napplicable law, without identifying or seeking Your\nconsent. Notwithstanding the foregoing, You acknowledge that BCCA\nand its licensors will retain or own all rights in and to any\npre-existing code or other technology, content and data that may be\nincorporated in the Improvements. For greater certainty, this\nSection applies solely to the Source Code and shall not give You\nany rights with respect to the object code or any other portion or\nformat of the Product which use, for greater certainty, is limited\nas set forth in this Agreement including as set out in Section 3(b)\nabove. You acknowledge and agree that you will provide copies of\nImprovements to BCCA in such format as reasonably requested by BCCA\nat any time upon the request of BCCA.\n\n6. CONFIDENTIALITY: You acknowledge that the Product is and\nincorporates confidential and proprietary information developed,\nacquired by or licensed to BCCA. You will take all reasonable\nprecautions necessary to safeguard the confidentiality of the\nProduct, and will not disclose any information about the Product to\nany other person without BCCA's prior written consent. You will\nnot allow the removal or defacement of any confidential or\nproprietary notice placed on the Product. You acknowledge that any\nbreach of this Section 6 will cause irreparable harm to BCCA and\nits licensors.\n\n7. NO WARRANTIES: THIS PRODUCT IS PROVIDED TO YOU BY BCCA IN ORDER TO\nALLOW YOU TO OBTAIN ACCESS TO LEADING ACADEMIC RESEARCH. THE PRODUCT\nIS PROVIDED TO YOU ON AN \"AS IS\" BASIS WITHOUT WARRANTY OF ANY\nKIND. NO WARRANTY, REPRESENTATION OR CONDITION EITHER EXPRESS OR\nIMPLIED, INCLUDING WITHOUT LIMITATION, ANY IMPLIED WARRANTY OR\nCONDITION OF MERCHANTABILITY, NON-INFRINGEMENT, PERFORMANCE,\nDURABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR USE SHALL\nAPPLY. BCCA DOES NOT WARRANT THAT THE PRODUCT WILL OPERATE ON A\nCONTINUOUS OR TROUBLE FREE BASIS.\n\n8. LIMITATION OF LIABILITY: TO THE MAXIMUM EXTENT PERMITTED BY\nAPPLICABLE LAW, IN NO EVENT SHALL THE AGGREGATE LIABILITY OF BCCA TO\nYOU EXCEED THE AMOUNT YOU HAVE PAID TO ACQUIRE THE PRODUCT (\"MAXIMUM\nAMOUNT\") AND WHERE YOU HAVE NOT PAID ANY AMOUNT FOR THE PRODUCT THEN\nTHE MAXIMUM AMOUNT SHALL BE DEEMED TO BE CDN$100.00. IN NO EVENT SHALL\nBCCA BE LIABLE FOR ANY INDIRECT, INCIDENTAL, CONSEQUENTIAL, OR SPECIAL\nDAMAGES, INCLUDING WITHOUT LIMITATION ANY DAMAGES FOR LOST PROFITS OR\nSAVINGS, REGARDLESS OF WHETHER THEY HAVE BEEN ADVISED OF THE\nPOSSIBILITY OF SUCH DAMAGE. EXCEPT TO THE EXTENT THAT THE LAWS OF A\nCOMPETENT JURISDICTION REQUIRE LIABILITIES BEYOND AND DESPITE THESE\nLIMITATIONS, EXCLUSIONS AND DISCLAIMERS, THESE LIMITATIONS, EXCLUSIONS\nAND DISCLAIMERS SHALL APPLY WHETHER AN ACTION, CLAIM OR DEMAND ARISES\nFROM A BREACH OF WARRANTY OR CONDITION, BREACH OF CONTRACT,\nNEGLIGENCE, STRICT LIABILITY OR ANY OTHER KIND OF CIVIL OR STATUTORY\nLIABILITY CONNECTED WITH OR ARISING FROM THIS AGREEMENT. YOU AGREE\nTHAT THE FOREGOING DISCLAIMER OF WARRANTIES AND LIMITATION OF\nLIABILITY ARE FAIR IN LIGHT OF THE NATURE OF THE RIGHTS GRANTED HEREIN\nAND THE AMOUNT OF FEES PAID BY YOU IN RESPECT OF THE PRODUCT.\n\n9. INDEMNITY: You will indemnify, defend and hold harmless BCCA, its\nboard of directors, staff and agents from and against any and all\nliability, loss, damage, action, claim or expense (including\nattorney's fees and costs at trial and appellate levels) in\nconnection with any claim, suit, action, demand or judgement\n(collectively, \"Claim\") arising out of, connected with, resulting\nfrom, or sustained as a result of Your use of the Product or the\ndownloading of the Product, including without limitation, any Claim\nrelating to infringement of BCCA's intellectual property rights or\nthe intellectual property rights of any third party.\n\n10. SUPPORT AND MAINTENANCE: You acknowledge and agree that, unless\nand to the extent expressly agreed by BCCA in a separate written\ndocument, the Product is provided to You without any support or\nmaintenance from BCCA and, for greater certainty, BCCA shall have\nno obligation to issue any update or upgrade to any Product.\n\n11. TERM: This Agreement is effective until terminated. You may\nterminate this Agreement at any time by ceasing use of the Product\nand destroying or deleting any copies of the Product. This\nAgreement will terminate immediately without notice from BCCA if\nYou fail to comply with any provision of this Agreement. BCCA may\nterminate this Agreement at any time upon notice to you where BCCA\ndetermines, in its sole discretion, that any continued use of the\nProduct could infringe the rights of any third parties. Upon\ntermination of this Agreement, and in any event upon BCCA\ndelivering You notice of termination, You shall immediately purge\nall Products from Your computer system(s), return to BCCA all\ncopies of the Product that are in Your possession or control, and\ncease any further development of any Improvements. On any\ntermination of this Agreement Sections 1, 4, 6, 7, 8, 9, 13 and 14\nshall survive such termination.\n\n12. GOVERNMENT END USERS: Where any of the Product is used, duplicated\nor disclosed by or to the United States government or a government\ncontractor or sub contractor, it is provided with RESTRICTED\nRIGHTS as defined in Title 48 CFR 52.227-19 and is subject to the\nfollowing: Title 48 CFR 2.101, 52.227-19, 227.7201 through\n227.7202-4, FAR 52.227-14, and FAR 52.227-19(c)(1-2) and (6/87),\nand where applicable, the customary software license, as described\nin Title 48 CFR 227-7202 with respect to commercial software and\ncommercial software documentation including DFAR 252.227-7013,\nDFAR 252,227-7014, DFAR 252.227-7015 and DFAR 252.7018, all as\napplicable.\n\n13. USE OF THE DOWNLOAD SERVICE: You acknowledge and agree that you\nwill be responsible for all costs, charges and taxes (where\napplicable) arising out of Your use of the Product and the\ndownloading of the Product. You acknowledge that You are\nresponsible for supplying any hardware or software necessary to\nuse the Product pursuant to this Agreement.\n\n14. GENERAL PROVISIONS:\n(a) This Agreement will be governed by the laws of the Province of\nBritish Columbia, and the laws of Canada applicable therein, excluding\nany rules of private international law that lead to the application of\nthe laws of any other jurisdiction. The United Nations Convention on\nContracts for the International Sale of Goods (1980) does not apply to\nthis Agreement. The courts of the Province of British Columbia shall\nhave non-exclusive jurisdiction to hear any matter arising in\nconnection with this Agreement.\n(b) USE OF THE PRODUCT IS PROHIBITED IN ANY JURISDICTION WHICH DOES\nNOT GIVE EFFECT TO THE TERMS OF THIS AGREEMENT.\n(c) You agree that no joint venture, partnership, employment,\nconsulting or agency relationship exists between You and BCCA as a\nresult of this Agreement or Your use of the Product.\n(d) You hereby consent to Your contact information and any other\npersonally identifiable information that You provide to us being\ndisclosed to and maintained and used by us and our business partners\nfor the purposes of (i) managing and developing our respective\nbusinesses and operations; (ii) marketing products and services to You\nand your staff; and (iii) developing new and enhancing existing\nproducts. You further agree that we may provide this information to\nother persons as required to satisfy any legal requirements and to any\nperson that acquires some or all of the assets of BCCA. Where any of\nthe personally identifiable information that You provide to us is in\nrespect of individuals other than Yourself (such as Your staff) then\nYou represent and warrant to use that You have obtained all necessary\nconsents and authorizations from such individuals in order to comply\nwith this provision. Please see the BCCA website for further\ninformation regarding personally identifiable information.\n(e) This Agreement is the entire Agreement between You and BCCA\nrelating to this subject matter. You will not contest the validity of\nthis Agreement merely because it is in electronic form. No\nmodification of this Agreement will be binding, unless in writing and\naccepted by an authorized representative of each party.\n(f) The provisions of this Agreement are severable in that if any\nprovision in the Agreement is determined to be invalid or\nunenforceable under any controlling body of law, that will not affect\nthe validity or enforceability of the remaining provisions of the\nAgreement.\n(g) You agree to print out or download a copy of this Agreement and\nretain it for Your records.\n(h) You consent to the use of the English language in this Agreement.\n(i) You may not assign this Agreement or any of Your rights or\nobligations hereunder without BCCA's prior written consent. BCCA, at\nits sole discretion may assign this Agreement without notice to You.\n\nFor commercial licensing options, please contact Patrick Rebstein prebstein@bccancer.bc.ca\n-----------------------------------------------------------\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbcgsc%2Fhlaminer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbcgsc%2Fhlaminer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbcgsc%2Fhlaminer/lists"}