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====== **__Main locations for most Databases on PERUN__** ======

/misc/db1/
    /scratch3/rogerlab_databases/other_dbs/
    /scratch4/db/
**BLAST databases**
    /db1/blast-may-2024/nr.pal (updated May 2024)
    /db1/blast-may-2024/refseq_protein.pal (updated May 2024)
    /db1/blast-may-2024/nt.nal  (updated May 2024)

/scratch3/rogerlab_databases/other_dbs/nr_010621
    /opt/perun/share/extra-data-sets/uniprot/ (updated Jul 25, 2017)
    /db1/extra-data-sets/MMETSP/MMETSP_db/ (2018, Kolisko et al. cleaned up with WinstoneCleaner see README file in he directory for more information)
    /opt/perun/share/extra-data-sets/CAM_P_0001000.nt.fa (old marine metagenome database)
** PLAST databases**
   /db1/extra-data-sets/nr-fasta.jun2024/nr.fasta (updated Jun, 2024)
   /scratch3/rogerlab_databases/other_dbs/nt_Jun2024/nt/nt.fasta (updated Jun, 2024)   
Note: Plast need to use the fasta file to run, and cannot use new format of v5 NCBI nr and nt databases
   
   
** DIAMOND:**
   /scratch3/rogerlab_databases/other_dbs/nr_March252023/diamond/nr.dmnd  (updated Mar 2023)
   /scratch3/rogerlab_databases/other_dbs/nr_032121/nr.dmnd  (updated Mar 2021)
   /scratch3/rogerlab_databases/other_dbs/nr_06162020/nr.dmnd  (updated Jun 2020)   
** CENTRIFUGE **
   /scratch2/software/centrifuge-1.0.3/  (updated 2019)
to use: the base index is "nt", which corresponds to the large nucleotide ncbi database in centrifuge format.

Centrifuge Database for Eukfinder:    
   /scratch3/Eukfinder/DB/Centrifuge_DB/
   the base index is Centrifuge_NewDB_Sept2020

** EGGNOG **
Several databases that are available at 
   /opt/perun/share/extra-data-sets/eggnog/
   /scratch4/db/eggnog-mapper-2.1.4/

**PRESSED databases  **
   Full archaea hmm profiles : archaea_DB.hmmer
   Full bacteria hmm profiles : BACT_DB.hmmer
   Full eukaryotes hmm profiles : EUK_DB.hmmer    
Virus and virus-like: 
         Picornavirales.hmmer, Retrotranscribing.hmmer, Retroviridae.hmmer, ssDNA.hmmer, ssRNA.hmmer, 
         ssRNA_negative.hmmer, ssRNA_positive.hmmer, Tymovirales.hmmer, Viruses.hmmer, Nidovirales.hmmer
if you need all domains together (bacteria, archaea and eukarya): 
      /opt/perun/share/extra-data-sets/eggnog/fulleggnogdb/fullEggNOGDB.hmmer
**NOT PRESSED (individual profiles):**\\
   hmm for bacteria at /opt/perun/share/extra-data-sets/eggnog/bactNOG_hmm
   hmm for archaea at /opt/perun/share/extra-data-sets/eggnog/arNOG_hmm
   hmm for eukaryotes at /opt/perun/share/extra-data-sets/eggnog/euNOG_hmm
   hmm for bacteria-archaea-eukaryotes at /opt/perun/share/extra-data-sets/eggnog/NOG_hmm   
**EggNOG ANNOTATIONS** are within each of the directories for individual profiles (Not pressed), except for NOG (NOG.annotations.tsv) which is in the 
   /opt/perun/share/extra-data-sets/eggnog

**PANTHER hmm database:**\\
PANTHER 17 Classification:
    /scratch3/rogerlab_databases/other_dbs/PANTHER17.0/
PANTHER fasta files by family:
   /scratch3/rogerlab_databases/other_dbs/PANTHER17.0/books (updated Jan 2022)

**EukProt:**

/scratch3/rogerlab_databases/other_dbs/EukProt_V3/proteins/  (updated Dec 2023)   
   /scratch4/db/EukProtv3/
   
**Kraken2:**

/scratch3/rogerlab_databases/other_dbs/kraken2/hash.k2d   (updated Nov 2023) 
    /scratch4/db/kraken2/
      
Most updated Kraken2 databases can be downloaded from here:
   https://benlangmead.github.io/aws-indexes/k2

**Acc2tax:**
   /db1/extra-data-sets/Acc2tax/

**Eukfinder**
   Acc2tax: /db1/extra-data-sets/Acc2tax/
            /scratch3/Eukfinder/DB/Acc2tax/
   Centrifuge: /scratch3/Eukfinder/DB/Centrifuge_DB/
   PLAST:      /scratch3/Eukfinder/DB/PLAST_DB/

**gtdbtk**
    gtdbtk-2.0.0: /scratch4/db/gtdbtk-2.0.0/ (Mar 2022)
    gtdbtk-2.0.0: /scratch4/db/gtdbtk-1.5.0/
    
<Last updated by Dandan Zhao on Sept 12, 2024>

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