Compare new datasets to UHGV (main figure)

[snayfach]

Main tasks

• [x] download all input datasets
• [x] run all through: checkv, viralverify, genomad, classiphi
• [x] load data
• [x] select contigs per study
• [x] make piecharts: uhgv and ictv classification
• [ ] add full set of genomes to db and see how it improves classification
• [ ] also screen contigs with genomad
• [x] make first panels giving overview
• [x] make piecharts smaller

[snayfach]

List of datasets:

• Archaeal Virome **
• Prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features linked to diets, populations, and diseases **
• Japanese 4D **
• Long read gut virome catalog
• Efficient recovery of complete gut phage genomes by combined short- and long-sequencing
• The gut virome in two indigenous populations from Malaysia
• Cataloguing and profiling of the gut virome in Chinese populations uncover extensive viral signatures across common diseases
• Insights into the Human Gut Virome by Sampling a Population from the Indian Subcontinent
• Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome
• https://www.nature.com/articles/s41564-019-0526-2
• https://www.nature.com/articles/s41467-021-27917-x#data-availability
• Yutin et al. crass like phages
• Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome
• Insights into the Human Gut Virome by Sampling a Population from the Indian Subcontinent

** selected dataset