New tool request: Host decontamination tools

[SaimMomin12]

• kneadata: New tool addition: KneadData #7498 (@xens25 is working on this)
• deacon/hostile https://github.com/bede (@SantaMcCloud is working on this) Add deacon and deacon DM #7473
• bmtagger https://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/ (@bernt-matthias will work on this) Add bmtagger #7451
• NEW!! Cleanifier

[SantaMcCloud]

I would work on deacon and maybe hostile if this okay? :)

[SantaMcCloud]

#7473 deacon PR

[bebatut]

https://github.com/mbhall88/nohuman could be interesting for Human reads:

During recent benchmarking, I found Kraken was detecting many more human reads than the nohuman database. It turns out Kraken masks low-complexity regions by default when building its DB and I had left this on when building the nohuman database.
Fix: I rebuilt everything without masking, and the difference is dramatic. I also took the opportunity to make a new database from the second release from the Human Pangenome Consortium (HPRC.r2)
| Pipeline / Database Used | Human reads detected |
|---------------------------------|----------------------|
| Kraken (standard DB) | 113,756 |
| nohuman (HPRC.r1 — masked) | 2,624 |
| nohuman (HPRC.r1 — unmasked) | 218,808 |
| nohuman (HPRC.r2 — unmasked) | 225,944 |
nohuman now includes support for selecting specific datasets
The unmasked HPRC.r2 database is now the default
Strongly recommend existing users update + redownload the DB
Repo: https://github.com/mbhall88/nohuman

[bernt-matthias]

Also recentrifuge seems to do decontamination (plus taxonomic classification)