Bart Nijsse
SEEK ID: https://workflowhub.eu/people/84
Location:
Netherlands
ORCID:
https://orcid.org/0000-0001-9524-5964
Joined: 23rd Nov 2020
Expertise: Not specified
Tools: Not specified
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, CO2MICS Lab, FAME, CHU Limoges - UF9481 Bioinformatique / CNR Herpesvirus, Quadram Institute Bioscience - Bioinformatics, HecatombDevelopment, Institute of Human Genetics, Testing RO Crates, Test Team, Applied Computational Biology at IEG/HMGU, INFRAFRONTIER workflows, OME, TransBioNet, OpenEBench, Galaxycompchem, Bioinformatics and Biostatistics (BIO2 ) Core
Web page: Not specified
An open infrastructure for exploring new horizons for research on microbial communities.
Workflow for sequencing with ONT nanopore, from basecalling to assembly quality. Steps:
- Kraken2 (taxonomic classification of FASTQ reads)
- Krona (classification visualization)
- Flye (de novo assembly)
- Medaka (assembly polishing)
- QUAST (assembly quality reports)
Type: Common Workflow Language
Creators: Bart Nijsse, Jasper Koehorst, Germán Royval
Submitter: Jasper Koehorst
DownloadWorkflow for sequencing with ONT nanopore, from basecalling to assembly quality. Steps:
- 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)
The dependencies are either accessible from https://unlock-icat.irods.surfsara.nl (anonymous) or by using the conda / pip environments as shown ...
Type: Common Workflow Language
Creators: Bart Nijsse, Jasper Koehorst, Germán Royval
Submitter: Jasper Koehorst
This workflow is dependent on other CWL workflows, see the git repository for these.
Workflow for Metagenomics from raw reads to annotated bins.
Main Steps
-
workflow_quality.cwl:
-
FastQC (control)
-
fastp (quality trimming)
-
bbmap contamination filter
-
SPAdes (Assembly)
-
QUAST (Assembly quality report)
-
BBmap (Read mapping to assembly)
-
MetaBat2 (binning)
-
CheckM (bin completeness and contamination)
-
GTDB-Tk (bin taxonomic classification)
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 for ngtax
Workflow 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)
