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POLYSOLVER / POLYmorphic loci reSOLVER
Enables high precision Human Leukocyte Antigen (HLA)-typing even. POLYSOLVER uses relatively low coverage whole exome sequencing (WES) data and a subsequent mutation detection pipeline that is based on the inferred alleles to detect mutations in HLA genes. The tool is able to infer HLA-type information with 97 per cent sensitivity and 98 per cent precision from exome-capture sequencing data. It can extract sequence and mutation information from other polymorphic regions in the genome.
HLA-MA
Permits to screen raw Illumina high-throughput sequencing (HTS) data for sample swaps for datasets where the Human Leukocyte Antigen (HLA) loci are covered. HLA-MA is based on the HLA typing result of the state-of-the-art method OptiType. It uses information from small but genetically highly variable regions and thus complements approaches that rely on genome or exon-wide variant profiles. The tool takes a relatively short time and can be run before or in parallel with the usual downstream processing.
HLA-VBSeq
An efficient and accurate human leucocyte antigen (HLA) typing method using high-throughput sequencing data without the need of primer design for HLA loci. In the first step of the HLA-VBSeq pipeline, read sequences are aligned to the reference genomic sequences of the registered HLA allelles in the IMGT/HLA database, in which multiple hits are allowed. Then, HLA-VBSeq optimizes both read alignments to the HLA allele sequences and relative quantities of reads on HLA alleles simultaneously under a statistical framework by variational Bayesian inference. Our approach considers all the possible alignments of reads to HLA allele sequences, and calculates the marginal likelihood of data from gapped alignments of reads to the reference sequences, in which deletions and insertions as well as SNP sites are naturally considered. It does not assume any prior knowledge about HLA allele frequencies, and hence HLA-VBSeq is broadly applicable to human samples obtained from a genetically diverse population.
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 locus and then computes the most likely set of haplotypes including their frequencies via the expectation-maximization (EM) algorithm. The software handles large-scale HLA genotype data. Its accuracy and performance were demonstrated on the basis of artificial and real genotype data.
PyHLA
Provides functions for association analysis, zygosity tests, and interaction tests between HLA alleles and diseases. PyHLA is a Python package which implements several methods for HLA association analysis, to fill the gap. It is a tailor-made, easy to use, and flexible tool designed specifically for the association analysis of the HLA types imputed from genome-wide genotyping and NGS data. This method is applicable to small and large sample sizes and can finish the analysis in a timely manner on a personal computer with different platforms. PyHLA is designed for case-control studies and is currently unable to analyze family-base datasets.
HLAscan
Performs alignment of reads to human leukocyte antigen (HLA) sequences from the international ImMunoGeneTics project (IMGT)/HLA database. HLAscan is an alignment-based multi-step HLA typing method considering read distribution. It outperforms the established next generation sequencing (NGS)-based methods but also may complement sequencing-based typing methods when dealing with high-depth (average 90×) short sequence reads. This method could be generally applied for variant calling in highly polymorphic regions.
Prohlatype
Provides a set of tools to calculate the full posterior distribution of human leukocyte antigen (HLA) types given read data. Prohlatype consists of: (i) downloading IMGT-HLA database, (ii) creating an imputed HLA reference sequences via the tool align2fasta, (iii) using the previously generated sequence database to filter user’s data via an aligner (iv) exporting the reads from the filtered bam file to a FASTQ file and (v) allowing users to calculate the likelihood with multi part.
Graphtyper
Allows to discover and genotype sequence variants in large populations using pangenome graphs. Graphtyper is a population-scale genotype caller. The software locally realigns sequence reads from a genomic region to a pangenome graph, and concomitantly genotypes sequence variants in all individuals. Using variation-aware realignment, it is capable of characterization of the region’s variation with no Mendelian errors and no falsely reported additional sequence variants around the indel.
HLA Completion
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Provides a method for statistical refinement of low or intermediate resolution HLA (Human Leucocyte Antigen) data, when a full resolution training data set from a similar population is available. HLA Completion tool introduces a methodology, improving upon the Expectation-Maximization (EM)-based approaches currently used within the HLA community. The improvements are achieved by using a parsimonious parameterization for haplotype distributions and by smoothing the maximum likelihood (ML) solution. These improvements make it possible to scale the refinement to a larger number of alleles and loci in a more computationally efficient and stable manner. This HLA refinement method helps to mitigate the limiting factor of cost in HLA typing, and allows for lower/intermediate resolution, or historical data to be statistically refined when it cannot be refined by assay.
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