OptiType protocols

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OptiType specifications

Information


Unique identifier OMICS_05461
Name OptiType
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License BSD 2-clause “Simplified” License
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline András Szolek <>

Publication for OptiType

OptiType in pipelines

 (5)
2018
PMCID: 5834292
PMID: 29541393
DOI: 10.18632/oncotarget.24232

[…] variant depth of ≥4, (iv) variant frequency in tumor of ≥10%, (v) variant frequency in normal of <2%, and (vi) fisher p value of <0.05. hla class i genotypes of the tumor were determined by optitype algorithm using whole-exome sequence data of normal dnas []. potential neoantigens were predicted for each non-synonymous mutation by testing all 8- to 11-mer peptides harboring the amino […]

2018
PMCID: 5905401
PMID: 29617672
DOI: 10.1016/j.celrep.2018.03.036

[…] the peptide sequence for the analyses and find recoding, he and pre-known sites filtered for snps and hla genes were annotated using wannovar (, ). hla alleles for each sample were derived using optitype (). for each sample, recoding sites (detected by the he analysis) inside peptides that have at least one window (see ) with strong affinity to the sample-predicted hla alleles were selected […]

2018
PMCID: 5922371
PMID: 29721177
DOI: 10.18632/oncotarget.24867

[…] ≥10%, (v) variant frequency in normal of <2%, and (vi) fisher p value of <0.05., using whole-exome sequence data of the germline dnas, hla class i genotypes of each patient were determined by optitype algorithm []. subsequently, neoantigens for each hla allele were predicted from non-synonymous mutations identified through the whole exome sequence data of 14 tumor samples. all 8- […]

2017
PMCID: 5617483
PMID: 28977923
DOI: 10.18632/oncotarget.18790

[…] annotated based on refgene using annovar as previously described [, ]., based on whole-exome sequence data from the germline dnas of breast cancer patients, hla class i genotypes were estimated by optitype algorithm []. then, non-synonymous somatic mutations identified through the whole-exome sequencing data of 15 tumor samples were utilized for the prediction of the hla genotypes-restricted […]

2016
PMCID: 5114739
PMID: 27855702
DOI: 10.1186/s13059-016-1092-z

[…] normal and/or tumor samples were processed to obtain fastq files. reads that aligned to hla-a, hla-b, or hla-c genes using razers3 [] (http://www.seqan.de/projects/razers/) were passed as input to optitype v1.0 [] (https://github.com/fred-2/optitype). discrepancies in hla typing were resolved by consensus or exclusion. a maf files containing missense mutations for each tcga patient […]


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OptiType in publications

 (12)
PMCID: 5899330
PMID: 29653567
DOI: 10.1186/s12885-018-4325-6

[…] its coordinates from the vcf file and the cds in the hg19 gene transfer format file [], and translating this sequence into amino acids. each patient’s hla type was determined from fastq files using optitype (v1.3.1) [], and the binding affinity of all predicted tumor and normal epitopes was predicted with netmhcpan (v2.8) [] for each epitope and patient-specific hla allele combination. […]

PMCID: 5905401
PMID: 29617672
DOI: 10.1016/j.celrep.2018.03.036

[…] the peptide sequence for the analyses and find recoding, he and pre-known sites filtered for snps and hla genes were annotated using wannovar (, ). hla alleles for each sample were derived using optitype (). for each sample, recoding sites (detected by the he analysis) inside peptides that have at least one window (see ) with strong affinity to the sample-predicted hla alleles were selected […]

PMCID: 5834780
PMID: 29288513
DOI: 10.1111/cas.13498

[…] which can bind to hla molecules. several tools have been developed to obtain hla allele information from genome‐wide sequencing data (whole‐exome, whole‐genome, and rna sequencing data), including optitype, polysolver, phlat, hlareporter, hlaforest, hlaminer, and seq2hla. we have tested 961 whole‐exome data from the 1000 genomes project to evaluate the accuracy of these programs. among […]

PMCID: 5778667
PMID: 29357823
DOI: 10.1186/s12885-017-3825-0

[…] in the case of frameshift mutations, all downstream peptides generated up to a stop codon were considered potential neoantigens., hla typing was performed using a consensus of seq2hla [] and optitype [] across the samples for each patient (additional file )., class i mhc binding predictions were performed for peptides of length 8–11 using netmhcpan 2.8 [] with default arguments […]

PMCID: 5733459
PMID: 29326702
DOI: 10.3389/fimmu.2017.01815

[…] the remaining alleles. the allele pair with the highest weighted harmonic mean of the scaled parameters is selected as the most likely allele pair. this is the allele pair we used for comparisons., optitype (), version 1.3.1, is a mapping-based method and can produce typings from both dna and rna sequencing data. it also aims at utilizing multi-mapping reads, whereas, in many other programs, […]


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OptiType institution(s)
Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Department of Computer Science, University of Tübingen, Institute of Medical Genetics and Applied Genomics, University of Tübingen, and CeGaT GmbH, Tübingen, Germany

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