Teams: Not specified
Organizations: Not specifiedhttps://orcid.org/0000-0002-1399-293X
Dad, husband and PhD. Scientist, technologist and engineer. Bibliophile. Philomath. Passionate about science, medicine, research, computing and all things geeky!
Teams: MAB - ATGC
Organizations: Centre National de la Recherche Scientifique (CNRS)https://orcid.org/0000-0003-1590-8313
Teams: MAB - ATGC
Organizations: Centre National de la Recherche Scientifique (CNRS)https://orcid.org/0000-0003-3791-3973
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:
Shotgun Metagenomics Analysis
Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more
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 ...
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 ...