Workflows

Transcripts annotation workflow

TransDecoder 2 step workflow, running TransDecoder.LongOrfs (step 1) followed by TransDecoder.Predict (step2)

Precision HLA typing from next-generation sequencing data using OptiType.

Table of Contents

Introduction Quick Start

With Docker With Singularity

Documentation Pipeline DAG

Input fastq Input bam

Credits

Introduction

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 ...