Jasper Koehorst
SEEK ID: https://workflowhub.eu/people/46
Location:
Netherlands
Expertise: Not specified
Tools: Not specified
https://orcid.org/0000-0001-8172-8981 
Team roles
Project administrator
Their tagsRelated items
A space managed by WorkflowHub administrators for teams that don't want/need to manage their own space.
Teams: IBISBA Workflows, NMR Workflow, UNLOCK, NanoGalaxy, Galaxy Climate, PNDB, IMBforge, COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource, LBI-RUD, Nick-test-team, usegalaxy-eu, Italy-Covid-data-Portal, UX trial team, Integrated and Urban Plant Pathology Laboratory, SARS-CoV-2 Data Hubs, lmjxteam2, virAnnot pipeline, Ay Lab, iPC: individualizedPaediatricCure, Harkany Lab, Genomics Coordination Center, EJPRD WP13 case-studies workflows, Common Workflow Language (CWL) community, Testing, SeBiMER, IAA-CSIC, MAB - ATGC, Probabilistic graphical models, GenX, Snakemake-Workflows, ODA, IPK BIT, lncRNA_workflowHub
Web page: Not specified
An open infrastructure for exploring new horizons for research on microbial communities.
Workflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2. In addition files are exported to their respective subfolders for easier data management in a later stage. Steps: - FastQC (read quality control) - NGTax 2.0 - Picrust 2 - Export module
DownloadWorkflow for Spliced RNAseq data Steps:
- workflow_quality.cwl:
- FastQC (Read Quality Control)
- fastp (Read Trimming)
- STAR (Read mapping)
- featurecounts (transcript read counts)
- kallisto (transcript [pseudo]counts)
Workflow for NonSpliced RNAseq data with multiple aligners.
Steps: - workflowquality.cwl: - FastQC (control) - fastp (trimming) - bowtie2 (read mapping) - samto_sorted-bam - featurecounts (transcript read counts) - kallisto (transcript [pseudo]counts)
Amplicon analysis workflow using NG-Tax
Steps:
- Quality control on the reads
- Execute NGTax for ASV detection and classification
For more information about NG-Tax 2.0 have a look at https://doi.org/10.3389/fgene.2019.01366
Type: Common Workflow Language
Creators: Jasper Koehorst, Bart Nijsse, Jesse van Dam, Peter Schaap,
Submitter: Jasper Koehorst
Workflow for (paired) read quality control, trimming and contamination filtering based on a given reference.
Will output a merged set of read pairs, when multiple datasets are used.
Steps:
FastQC (read quality control)
fastp (read quality trimming)
bbduk used (rrna filtering)
bbmap (contamination filter)
