RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Nextflow training material for introductory tutorial

Nextflow pipeline for Mutect2 somatic variant calling best practices

Mutect pipeline with Nextflow

Variant calling pipeline for the Illumina Dragen platform

Pipeline for RNA and DNA integrated analysis for somatic mutation detection

Single cell transcriptome analysis pipeline based on DropEst