Workflows
HiFi de novo genome assembly workflow
HiFi-assembly-workflow is a bioinformatics pipeline that can be used to analyse Pacbio CCS reads for de novo genome assembly using PacBio Circular Consensus Sequencing (CCS) reads. This workflow is implemented in Nextflow and has 3 major sections.
Please refer to the following documentation for detailed description of each workflow section:
- Pre-assembly quality control (QC)
- Assembly
- Post-assembly QC
HiFi assembly workflow flowchart
![flow chart ...
Workflow Kallisto RNAseq
- Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1
- kallisto (pseudoalignment on transcripts)
All tool CWL files and other workflows can be found here: Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows
The dependencies are either accessible from https://unlock-icat.irods.surfsara.nl (anonymous,anonymous) and/or By using the conda / pip environments as shown in ...
A workflow for the quality assessment of mass spectrometry (MS) based proteomics analyses
Workflow for Illumina paired read quality control, trimming and filtering. Multiple paired datasets will be merged into single paired dataset. Summary:
- FastQC on raw data files
- fastp for read quality trimming
- BBduk for phiX and (optional) rRNA filtering
- Kraken2 for taxonomic classification of reads (optional)
- BBmap for (contamination) filtering using given references (optional)
- FastQC on filtered (merged) data
All tool CWL files and other workflows can be found here: Tools: ...
StructuralVariants Workflow
Type: Common Workflow Language
Creators: Laura Rodriguez-Navas, Daniel López-López
Submitter: Laura Rodriguez-Navas
GermlineShortV_biovalidation
Type: Shell Script
Creators: Georgina Samaha, Tracy Chew, Cali Willet, Nandan Deshpande
Submitter: Georgina Samaha
Objective. Biomarkers have become important for the prognosis and diagnosis of various diseases. High-throughput methods such as RNA-sequencing facilitate the detection of differentially expressed genes (DEGs), hence potential biomarker candidates. Individual studies suggest long lists of DEGs, hampering the identification of clinically relevant ones. Concerning preeclampsia, a major obstetric burden with high risk for adverse maternal and/or neonatal outcomes, limitations in diagnosis and ...