Optitype paired-end
WebNGS-based HLA typing algorithm. Container. Pulls 10K+ Overview Tags. Dockerfile ################################################################# # Dockerfile ... WebSep 9, 2024 · If it's used in the pipeline, it comes in the pipeline container (s) (or conda environment or whatever packaging system you use). So you should never have to touch docker://fred2/optitype. When you run the pipeline with the -profile singularity argument, it will automatically pull the image from Docker Hub and convert to Singularity for you ...
Optitype paired-end
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WebMay 20, 2024 · For both WES data and RNA-seq data, OptiType showed the highest accuracy for HLA-Ia typing than the other 3 programs at 2-digit and 4-digit resolution. Additionally, HLA typing accuracy from WES data was higher than from RNA-seq data (99.11% for WES data versus 96.42% for RNA-seq data). The accuracy of HLA-Ia typing by OptiType can … WebNov 12, 2024 · Here, we present nextNEOpi ( next flow NEO antigen prediction pi peline), a fully automated and comprehensive computational workflow that overcomes these shortcomings. nextNEOpi predicts class-I and -II neoantigens originating from SNVs, indels and gene fusions through the analysis of raw sequencing data and derives a set of …
Web2 hours ago · With Oklahoma City's season officially coming to an end on Friday night, the team can focus on finding the next piece to help get OKC reach another level of postseason success. WebOptiTypeis a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by …
WebJun 10, 2024 · OptiType is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles. Environment Modules Run module spider optitype to find out what environment modules are available …
WebMar 1, 2024 · In PGNneo, four modules are included: (1) noncoding somatic variant calling and HLA typing; (2) peptide extraction and customized database construction; (3) variant peptide identification; (4) neoantigen prediction and selection. tsm f1WebJan 8, 2015 · OptiType is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from … phim the fabelmansWebJan 1, 2014 · To this end, OptiType u ses recon structed in tron seque nces for pa rtially. ... Applying Op tiType on all 253 paired-end Il lumina exom e. sequenci ng runs of the 10 00 … phim the exceptionWebJun 25, 2024 · Optitype identifies reads that map to exons 2 and 3 of the HLA class I alleles to select the most likely HLA class I allele from a custom database. Similarly, Polysolver [ 33] relies on a Bayesian probabilistic model to reassign reads that failed to map to the consensus reference genome. phim the fabulousWebSep 30, 2024 · Genomic analysis of paired tumor–normal samples and clinical data can be used to match patients to cancer therapies or clinical trials. We analyzed 500 patient samples across diverse tumor types... phim the expanseWebNational Center for Biotechnology Information phim the fableWebJan 1, 2014 · Opti-Type has been reported to be one of the best and most widely used methods for HLA typing [49]. ... Neoepitopes prediction strategies: an integration of cancer genomics and immunoinformatics... phim the exit