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 ...

Workflow for Metagenomics from raw reads to annotated bins. Summary

• MetaBAT2 (binning)
• CheckM (bin completeness and contamination)
• GTDB-Tk (bin taxonomic classification)
• BUSCO (bin completeness)

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 ...

Workflow for sequencing with ONT Nanopore, from basecalling to assembly.

• Guppy (basecalling of raw reads)
• MinIONQC (quality check)
• FASTQ merging from multi into one file
• Kraken2 (taxonomic classification)
• Krona (classification visualization)
• Flye (de novo assembly)
• Medaka (assembly polishing)
• QUAST (assembly quality reports)

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 ...

Workflow for nanopore read quality control and contamination filtering.

• FastQC before filtering (read quality control)
• Kraken2 taxonomic read classification
• Minimap2 read filtering based on given references
• FastQC after filtering (read quality control)

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

WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default ...

ESCALIBUR

Escalibur Population Genomic Analysis Pipeline is able to explore key aspects centering the population genetics of organisms, and automates three key bioinformatic components in population genomic analysis using Workflow Definition Language (WDL: https://openwdl.org/), and customised R, Perl, Python and Unix shell scripts. Associated programs are packaged into a platform independent singularity image, for which the definition file is provided.

The workflow for analysis using Escalibur ...

CWL based workflow to assemble haploid/diploid eukaryote genomes of non-model organisms

The workflow is designed to use both PacBio long-reads and Illumina short-reads. The workflow first extracts, corrects, trims and decontaminates the long reads. Decontaminated trimmed reads are then used to assemble the genome and raw reads are used to polish it. Next, Illumina reads are cleaned and used to further polish the resultant assembly. Finally, the polished assembly is masked using inferred repeats ...