Construct databases for all profilers from the same input refseq data

[LilyAnderssonLee]

Construct databases using the same refseq data as the kraken2 database which includes

• complete genome, chromosome, scaffold and contigs
• Archaea, Bacteria, viral, protozoa, fungi, plasmid, human (GRCh38 &T2T), UniVec_Core

kraken2 database can be downloaded from https://benlangmead.github.io/aws-indexes/k2

The list of refseq sequences is stored in the tsv file: https://genome-idx.s3.amazonaws.com/kraken/pluspf_20231009/library_report.tsv

Update databases whenever the kraken2 database is updated.

This issue can be closed after construction of these databases:

• [x] diamond
• [x] kaiju
• [ ] centrifuge
• [ ] krakenuniq
• [ ] kmcp
• [ ] ganon
• [ ] sourmash

[LilyAnderssonLee]

kaiju The db construction failed due the memory limit, 450GB on hasta. This database was built on UPPMAX Bianca with 512GB memory.