Add kente to the pipeline

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Goal/plan

Link: kente.
Use: Kente is a pangenome graph–based framework for detecting horizontal gene transfer (HGT) from assembled metagenomic contigs.

• Include this in the genome-dynamics subworkflow for HGT detection. Focus on single sample whereas rhea does longitudinal.

Details

DB

• Download the DB from Zenodo (zipped ~ 2.5 GB; unzipped 9 GB)
• Can use the local version from here, says Natalie: /home/Users/nk62/Projects/HGT_pangenome/scripts_new/kente_pangenome_graph_database_v1.0.zip

Test dataset

• Provided in the Zenodo link
• How long does it take to run on your test dataset: example_contigs.fna

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Progress:

Notes