seq2HLA specifications

Information


Unique identifier OMICS_02152
Name seq2HLA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Some RNA-Seq sequence reads.
Input format FASTQ
Output data The most likely HLA class I and class II types, a P-value for each call, and the expression of each class.
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Programming languages Python, R
Computer skills Advanced
Version 2.2
Stability Stable
Maintained Yes

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Publication for seq2HLA

seq2HLA in publications

 (10)
PMCID: 5872580
PMID: 29587858
DOI: 10.1186/s12920-018-0354-x

[…] the reference does not reflect the polymorphic nature of the hla system, precluding accurate hla typing [] and thus expression determination. to account for this, we developed the algorithm ‘seq2hla’ [] that takes bulk rna-seq raw data as input and outputs the most probable 4-digit hla class i and ii types [] and locus-specific expression., here, we extended seq2hla to determine the hla […]

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

[…] 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 these algorithms, optitype showed the highest accuracy of 97.2% for hla […]

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

[…] substitution). 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 […]

PMCID: 5778604
PMID: 29403468
DOI: 10.3389/fimmu.2017.01807

[…] the patient’s hla type. this can be determined computationally from exome or bulk rna sequencing or validated externally using hla-specific amplicon sequencing (). the pgv pipeline currently uses seq2hla () for hla typing from tumor rna while also using amplicon sequencing of normal dna for validation. across 10 patients, the two methods have only disagreed on a single allele, […]

PMCID: 5828548
PMID: 29269040
DOI: 10.1016/j.ebiom.2017.11.031

[…] the variant discovery. finally, variant discovery was performed by unifiedgenotyper module. the module used bayesian genotype likelihood model to call the variants. hla-typing was performed using seq2hla_ver2.2 ()., the search tool for the retrieval of interacting genes/proteins (string) (http://string.embl.de/) was used to identify known and predicted interactions among the differential […]


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seq2HLA institution(s)
TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Mainz, Germany; University Medical Center of the Johannes Gutenberg University Mainz, III, Medical Department, Mainz, Germany; Ganymed Pharmaceuticals AG, Mainz, Germany

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