{"repo":"nf-core/hlatyping","free":true,"listed":false,"github":"https://github.com/nf-core/hlatyping","clone":"git clone https://github.com/nf-core/hlatyping.git","description":"Precision HLA typing from next-generation sequencing data","language":"Nextflow","stars":81,"topics":["hla","hla-typing","immunology","dna","rna","optitype","personalized-medicine","nf-core","nextflow","workflow"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/hlatyping is a bioinformatics pipeline that can be used to perform HLA typing from next-generation sequencing data. The pipeline does next-generation sequencing-based Human Leukocyte Antigen (HLA) typing using OptiType. OptiType is a HLA genotyping algorithm based on integer linear programming. Reads of whole exome/genome/transcriptome sequencing data are mapped against a reference of known MHC class I alleles. To produce accurate 4-digit HLA genotyping predictions, all major and minor HLA-I loci are considered simultaneously to find an allele combination that maximizes the number of explained reads. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of resul","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/hlatyping/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}