Fix - Pathogen detection from (direct Nanopore) sequencing data using Galaxy
Opened this issue · 1 comments
paulzierep commented
There are some issues with this training that I collect here to fix step-by-step.
- In the preprocessing part, all fastq outputs go into multiQC, but since multiQC only shows one output for identically named files, this is rather useless. Either fix multiQC, rename the files or run in twice.
- The preprocessing WF (https://github.com/galaxyproject/training-material/blob/main/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/nanopore_preprocessing.ga) contains some parts which are not part of the training (Host Sequences Detection and Removal (Mapping Technique) and (Creating a table for samples reads count before and after hosts sequences removal and the percentage of found hosts sequences)
Assign filted reads, after mapping (non chicken reads), to taxa using Kraken2 ([Wood and Salzberg 2014](https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html#Wood2014)) and Kalamari, a database of completed assemblies for metagenomics-related tasks used widely in contamination and host filtering-> this is not correct