Research Object Crate for Long Read WGS pipeline

Original URL: https://workflowhub.eu/workflows/1868/ro_crate?version=1

**Workflow for long read quality control, contamination filtering, assembly, variant calling and annotation.** Steps: - Preprocessing of reference file : https://workflowhub.eu/workflows/1818 - LongReadSum before and after filtering (read quality control) - Filtlong filter on quality and length - Flye assembly - Minimap2 mapping of reads and assembly - Clair3 variant calling of reads - Freebayes variant calling of assembly - Optional Bakta annotation of genomes with no reference - SnpEff building or downloading of a database - SnpEff functional annotation - Liftoff annotation lift over **All tool CWL files and other workflows can be found here:** Tools: https://git.wur.nl/ssb/automated-data-analysis/cwl/-/tree/main/tools Workflows: https://git.wur.nl/ssb/automated-data-analysis/cwl/-/tree/main/workflows

Author: Martijn Melissen
License: CC-BY-4.0

Main Workflow: Long Read WGS pipeline
Size: 34338 bytes

Main Workflow Diagram: pipeline_diagram.png
Size: 51271 bytes

Main Workflow Description: workflow_ada_packed.cwl
Size: 318436 bytes

Research Object Crate for Long Read WGS pipeline

Contents