PMID- 30942877
OWN - NLM
STAT- MEDLINE
DCOM- 20200630
LR  - 20220129
IS  - 1367-4811 (Electronic)
IS  - 1367-4803 (Print)
IS  - 1367-4803 (Linking)
VI  - 35
IP  - 21
DP  - 2019 Nov 1
TI  - HLA*LA-HLA typing from linearly projected graph alignments.
PG  - 4394-4396
LID - 10.1093/bioinformatics/btz235 [doi]
AB  - SUMMARY: HLA*LA implements a new graph alignment model for human leukocyte 
      antigen (HLA) type inference, based on the projection of linear alignments onto a 
      variation graph. It enables accurate HLA type inference from whole-genome (99% 
      accuracy) and whole-exome (93% accuracy) Illumina data; from long-read Oxford 
      Nanopore and Pacific Biosciences data (98% accuracy for whole-genome and targeted 
      data) and from genome assemblies. Computational requirements for a typical sample 
      vary between 0.7 and 14 CPU hours per sample. AVAILABILITY AND IMPLEMENTATION: 
      HLA*LA is implemented in C++ and Perl and freely available as a bioconda package 
      or from https://github.com/DiltheyLab/HLA-LA (GPL v3). SUPPLEMENTARY INFORMATION: 
      Supplementary data are available at Bioinformatics online.
CI  - (c) The Author(s) 2019. Published by Oxford University Press.
FAU - Dilthey, Alexander T
AU  - Dilthey AT
AD  - Institute of Medical Microbiology, University Hospital of Dusseldorf, Dusseldorf, 
      North Rhine-Westphalia, Germany.
AD  - Genome Informatics Section, Computational and Statistical Genomics Branch, 
      National Human Genome Research Institute, Bethesda, MD, USA.
AD  - Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
FAU - Mentzer, Alexander J
AU  - Mentzer AJ
AD  - Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
AD  - Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, 
      University of Oxford, Oxford, UK.
FAU - Carapito, Raphael
AU  - Carapito R
AD  - Laboratoire d'ImmunoRhumatologie Moleculaire, Plateforme GENOMAX, INSERM UMR_S 
      1109, LabEx TRANSPLANTEX, Federation de Medecine Translationnelle de Strasbourg 
      (FMTS), Faculte de Medecine, Universite de Strasbourg, France.
AD  - Service d'Immunologie Biologique, Nouvel Hopital Civil, Strasbourg, France.
FAU - Cutland, Clare
AU  - Cutland C
AD  - Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, 
      Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South 
      Africa.
AD  - Department of Science/National Research Foundation: Vaccine Preventable Diseases, 
      Faculty of Health Science, University of the Witwatersrand, Johannesburg, South 
      Africa.
FAU - Cereb, Nezih
AU  - Cereb N
AD  - Histogenetics, Ossining, NY, USA.
FAU - Madhi, Shabir A
AU  - Madhi SA
AD  - Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, 
      Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South 
      Africa.
AD  - Department of Science/National Research Foundation: Vaccine Preventable Diseases, 
      Faculty of Health Science, University of the Witwatersrand, Johannesburg, South 
      Africa.
FAU - Rhie, Arang
AU  - Rhie A
AD  - Genome Informatics Section, Computational and Statistical Genomics Branch, 
      National Human Genome Research Institute, Bethesda, MD, USA.
FAU - Koren, Sergey
AU  - Koren S
AD  - Genome Informatics Section, Computational and Statistical Genomics Branch, 
      National Human Genome Research Institute, Bethesda, MD, USA.
FAU - Bahram, Seiamak
AU  - Bahram S
AD  - Laboratoire d'ImmunoRhumatologie Moleculaire, Plateforme GENOMAX, INSERM UMR_S 
      1109, LabEx TRANSPLANTEX, Federation de Medecine Translationnelle de Strasbourg 
      (FMTS), Faculte de Medecine, Universite de Strasbourg, France.
AD  - Service d'Immunologie Biologique, Nouvel Hopital Civil, Strasbourg, France.
FAU - McVean, Gil
AU  - McVean G
AD  - Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
AD  - Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, 
      University of Oxford, Oxford, UK.
FAU - Phillippy, Adam M
AU  - Phillippy AM
AD  - Genome Informatics Section, Computational and Statistical Genomics Branch, 
      National Human Genome Research Institute, Bethesda, MD, USA.
LA  - eng
GR  - WT_/Wellcome Trust/United Kingdom
GR  - 294557/ERC_/European Research Council/International
GR  - 106289/Z/14/Z/WT_/Wellcome Trust/United Kingdom
PT  - Journal Article
PT  - Research Support, N.I.H., Intramural
PT  - Research Support, Non-U.S. Gov't
PL  - England
TA  - Bioinformatics
JT  - Bioinformatics (Oxford, England)
JID - 9808944
SB  - IM
MH  - Genome
MH  - *High-Throughput Nucleotide Sequencing
MH  - Histocompatibility Testing
MH  - Humans
MH  - Sequence Analysis, DNA
MH  - *Software
PMC - PMC6821427
EDAT- 2019/04/04 06:00
MHDA- 2020/07/01 06:00
PMCR- 2019/04/03
CRDT- 2019/04/04 06:00
PHST- 2018/10/26 00:00 [received]
PHST- 2019/02/26 00:00 [revised]
PHST- 2019/04/02 00:00 [accepted]
PHST- 2019/04/04 06:00 [pubmed]
PHST- 2020/07/01 06:00 [medline]
PHST- 2019/04/04 06:00 [entrez]
PHST- 2019/04/03 00:00 [pmc-release]
AID - 5426702 [pii]
AID - btz235 [pii]
AID - 10.1093/bioinformatics/btz235 [doi]
PST - ppublish
SO  - Bioinformatics. 2019 Nov 1;35(21):4394-4396. doi: 10.1093/bioinformatics/btz235.