Nextflow-NGS

Generic pipelines for next-generation sequencing data analysis using Nextflow. These pipelines comprise robust and reasonable tool selection for various analysis steps.

File conversion

• SRA conversion - File conversion of *.sra files from the Read Sequencing Archive to regular fastq-files using sra-tools.

Preprocessing

• Adapter trimming - Standard adapter trimming and QC using trim_galore

Genome tools

• Mappability - Genome-wide mappability assessment using the GEM-library

Mapping

• star_align - VBCF RNA-seq alignment and QA pipeline using STAR
• ChIPSeq_align - VBCF ChIP-seq alignment and QA pipeline using bowtie

Variant calling

• GATK RNA-Seq - Variant calling on RNA-Seq data using Broad's Genome Analysis Toolkit following their best practices.

Peak calling

• SICER - Standard broad peak calling using SICER.
• MACS2 - Standard general peak calling using MACS2.
• SWEMBL - Standard tight peak calling using SWEMBL.
• SNSPeak - Calling of initiation sites (IS) and initation zones (IZ) according to Cayrou et al, Genome Research 2015.
• SNSPeakMACS - Calling of initiation sites (IS) and initation zones (IZ) using MACS2.