Generic pipelines for next-generation sequencing data analysis using Nextflow. These pipelines comprise robust and reasonable tool selection for various analysis steps.
- SRA conversion - File conversion of *.sra files from the Read Sequencing Archive to regular fastq-files using sra-tools.
- Adapter trimming - Standard adapter trimming and QC using trim_galore
- Mappability - Genome-wide mappability assessment using the GEM-library
- star_align - VBCF RNA-seq alignment and QA pipeline using STAR
- ChIPSeq_align - VBCF ChIP-seq alignment and QA pipeline using bowtie
- GATK RNA-Seq - Variant calling on RNA-Seq data using Broad's Genome Analysis Toolkit following their best practices.
- 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.