https://orcid.org/0000-0002-4405-6802I am a bioinformatician working on microbial ecology and ecosystem functioning at the microbial dimension.
Dad, husband and PhD. Scientist, technologist and engineer. Bibliophile. Philomath. Passionate about science, medicine, research, computing and all things geeky!
Workflow for sequencing with ONT Nanopore data, from basecalled reads to (meta)assembly and binning
- Workflow Nanopore Quality
- Kraken2 taxonomic classification of FASTQ reads
- Flye (de-novo assembly)
- Medaka (assembly polishing)
- metaQUAST (assembly quality reports)
When Illumina reads are provided:
- Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1
- Assembly polishing with Pilon
- Workflow binnning https://workflowhub.eu/workflows/64?version=11
- Metabat2 ...
Type: Common Workflow Language
Creators: Bart Nijsse, Jasper Koehorst, Germán Royval
Submitter: Jasper Koehorst
Shotgun Metagenomics Analysis
Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more
Description
The input for this analysis is paired end next generation sequencing data from metagenomic samples. The workflow is designed to be modular, so that individual modules can be run depending on the nature of the metagenomics project at hand. More modules will be added as we develop them - this repo is a work in progress!
These scripts have been written ...
Type: Shell Script
Creators: Cali Willet, Rosemarie Sadsad, Tracy Chew, Smitha Sukumar, Elena Martinez, Christina Adler, Henry Lydecker, Fang Wang
Submitter: Tracy Chew
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 ...
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