Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

HLA typing software tools | RNA sequencing data analysis

The human leukocyte antigen (HLA) gene cluster plays a crucial role in adaptive immunity and is thus relevant in many biomedical applications. While next-generation sequencing data are often available for a patient, deducing the HLA genotype is…
G T A T C G C T A
TIminer
Desktop

TIminer Tumor Immunology miner

Performs integrative immunogenomic analyses using next generation sequencing…

Performs integrative immunogenomic analyses using next generation sequencing (NGS) data. TIminer analyzes single-sample RNA-seq data and somatic DNA mutations to characterize the tumor-immune…

G T A T C G C T A
HLAProfiler
Desktop

HLAProfiler

Determines human leukocyte antigen (HLA) types using RNA-seq data. HLAProfiler…

Determines human leukocyte antigen (HLA) types using RNA-seq data. HLAProfiler employs the k-mer content of RNA-seq reads to identify the most likely HLA type for the sample. It is able to correctly…

G T A T C G C T A
seq2HLA
Desktop

seq2HLA

A method for obtaining an individualXs HLA class I and II type and expression…

A method for obtaining an individualXs HLA class I and II type and expression using standard NGS RNA-Seq data. Because the algorithm uses standard RNA-Seq reads and requires no change to laboratory…

G T A T C G C T A
Hapl-o-Mat
Desktop

Hapl-o-Mat

Allows human leucocyte antigen (HLA) haplotype frequency estimation. Hapl-o-Mat…

Allows human leucocyte antigen (HLA) haplotype frequency estimation. Hapl-o-Mat preprocesses the input genotype data, resolves genotyping ambiguities, translates alleles to a uniform resolution per…

G T A T C G C T A
OptiType
Desktop

OptiType

A HLA genotyping algorithm based on integer linear programming, capable of…

A HLA genotyping algorithm based on integer linear programming, capable of producing accurate predictions from NGS data not specifically enriched for the HLA cluster. OptiType significantly…

G T A T C G C T A
HLATyphon
Desktop

HLATyphon

A NGS data analysis pipeline allowing user to make HLA alleles genotyping…

A NGS data analysis pipeline allowing user to make HLA alleles genotyping quickly and efficiently. HLATyphon supports all cDNA template of HLA locus A, B, C, DPA1, DPB1, DQA1, DQB1 and DRB1 in…

G T A T C G C T A
PHLAT
Desktop

PHLAT

A tool algorithm named to discover the most probable pair of HLA alleles at…

A tool algorithm named to discover the most probable pair of HLA alleles at four-digit resolution or higher, via a unique integration of a candidate allele selection and a likelihood scoring. PHLAT…

G T A T C G C T A
Omixon Target…
Desktop

Omixon Target HLA Typing

Gives high resolution results with whole genome, exome or very targeted DNA…

Gives high resolution results with whole genome, exome or very targeted DNA data, or with RNA seq data. Omixon Target HLA Typing offers high possible HLA typing precision using NGS data. There is no…

G T A T C G C T A
HLAminer
Desktop

HLAminer

A software for HLA class I and II predictions from next-generation shotgun…

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. This approach…

G T A T C G C T A
HLAforest
Desktop

HLAforest

Predicts HLA haplotype by hierarchically weighting reads and using an…

Predicts HLA haplotype by hierarchically weighting reads and using an iterative, greedy, top down pruning technique. HLAforest uses BioPerl to read in FASTA files. Alignments use Bowtie, although any…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.