Pipelines Reference Guide

GenPipes implements standardized genomics workflows, including DNA-Seq, tumour analysis, RNA-Seq, de novo RNA-Seq, ChIP-Seq, SARS-CoV-2 genome sequencing, methylation sequencing, Hi-C, capture Hi-C, and metagenomics. All pipelines have been implemented following a robust design and development routine by following established best practices standard operating protocols. The pipelines accept a binary sequence alignment map (BAM) or a FASTQ file as input.

This guide contains usage manual and reference information for all available GenPipes genomic analysis pipelines. Visit GenPipes Real-life Applications and use cases to see how these pipelines can be deployed for complex next-generation genomic analysis in real life scenarios.

• Amplicon Sequencing Pipeline
• ChIP Sequencing Pipeline
• CoV Sequencing Pipeline
• DNA Sequencing Pipeline
• DNA Sequencing (High Coverage) Pipeline
• EpiQC Pipeline
• HiC Sequencing Pipeline
• Methylation Sequencing Pipeline
• Nanopore Pipeline
• Nanopore CoVSeQ Pipeline
• RNA Sequencing Pipeline
• De-Novo RNA Sequencing Pipeline
• RNA Sequencing (Light) Pipeline
• Tumor Pair Sequencing Pipeline