Adding Submodule - Gene prediction and annotation for mapped reads

jhuapl-bio / taxtriage

TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomic NGS data. This flexible tool was developed with various use-cases of mNGS in mind.

MIT License

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Adding Submodule - Gene prediction and annotation for mapped reads #42

Closed Merritt-Brian closed 7 months ago

Merritt-Brian commented 10 months ago

Description of feature

Currently, Kraken2 reports a relatively large number of positives that are false for certain bacteria in messy sample types like stool. Consider adding GFF's into the mix for ensuring that CDS regions are being properly mapped and that there is enough breadth in coverage. Also consider filtering down to only important annotations such as AMR, virulence, pathogenicity etc.

Merritt-Brian commented 7 months ago

This currently is implemented but cant take >80GB of RAM for general data. Not recommended. Use --skip_features for now to disable this

Merritt-Brian commented 7 months ago

Completed in release https://github.com/jhuapl-bio/taxtriage/releases/tag/v1.3.0