metaphlan

#http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/
mkdir -p reference/metaphlan
cd reference/metaphlan
wget http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103.tar
wget http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103_marker_info.txt.bz2
wget http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_vJan21_CHOCOPhlAnSGB_202103_species.txt.bz2
tar xvf mpa_vJan21_CHOCOPhlAnSGB_202103.tar
bunzip2 *.bz2
bowtie2-build mpa_vJan21_CHOCOPhlAnSGB_202103_SGB.fna mpa_vJan21_CHOCOPhlAnSGB_202103_SGB

metaphlan/
├── mpa_vJan21_CHOCOPhlAnSGB_202103_SGB.1.bt2
├── mpa_vJan21_CHOCOPhlAnSGB_202103_SGB.2.bt2
├── mpa_vJan21_CHOCOPhlAnSGB_202103_SGB.3.bt2
├── mpa_vJan21_CHOCOPhlAnSGB_202103_SGB.4.bt2
├── mpa_vJan21_CHOCOPhlAnSGB_202103_SGB.fna
├── mpa_vJan21_CHOCOPhlAnSGB_202103_SGB_marker_info.txt
├── mpa_vJan21_CHOCOPhlAnSGB_202103_SGB.pkl
├── mpa_vJan21_CHOCOPhlAnSGB_202103_SGB.rev.1.bt2
└── mpa_vJan21_CHOCOPhlAnSGB_202103_SGB.rev.2.bt2

CARD

#https://github.com/arpcard/rgi#load-card-reference-data
mkdir -p reference/CARD
cd reference/metaphlan
wget https://card.mcmaster.ca/latest/data
tar -xvf data card.json
rgi load --card_json card.json --local
rgi card_annotation -i card.json
rgi load -i card.json --card_annotation card_database_v3.0.1.fasta --local
wget -O wildcard_data.tar.bz2 https://card.mcmaster.ca/latest/variants
mkdir -p wildcard
tar -xjf wildcard_data.tar.bz2 -C wildcard
gunzip wildcard/*.gz
rgi wildcard_annotation -i wildcard --card_json card.json -v version_number
rgi load --wildcard_annotation wildcard_database_v3.0.2.fasta --wildcard_index /path/to/wildcard/index-for-model-sequences.txt --card_annotation card_database_v3.0.1.fasta --local

CARD/
├── card.json
└── localDB
    ├── 61mer_database.json
    ├── amr_61mer.txt
    ├── bwt
    ├── card.json
    ├── card_reference.fasta
    ├── card_wildcard_reference.fasta
    ├── index-for-model-sequences.txt
    └── loaded_databases.json

Kraken2

Kraken Wiki:https://github.com/DerrickWood/kraken2/wiki
Kraken index: https://benlangmead.github.io/aws-indexes/k2

mkdir -p reference/kraken2
cd reference/kraken2
wget https://genome-idx.s3.amazonaws.com/kraken/k2_pluspf_16gb_20220908.tar.gz

kraken2
├── database100mers.kmer_distrib
├── database150mers.kmer_distrib
├── database200mers.kmer_distrib
├── database250mers.kmer_distrib
├── database300mers.kmer_distrib
├── database50mers.kmer_distrib
├── database75mers.kmer_distrib
├── hash.k2d
├── inspect.txt
├── opts.k2d
├── seqid2taxid.map
└── taxo.k2d

human_phinx_index(host index)

mkdir -p reference/human_phinx_index/
# download phinx from NCBI
https://www.ncbi.nlm.nih.gov/nuccore/NC_001422
# download human genome sequence from gencode
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/GRCh38.p13.genome.fa.gz
cd reference/human_phinx_index/
cat GRCh38.p13.genome.fa.gz NC_001422.fasta >host.fasta
bowtie2-build host.fasta host.fasta

human_phix_index/
├── GRCh38.p13.genome.fa
├── host.fasta
├── host.fasta.1.bt2
├── host.fasta.2.bt2
├── host.fasta.3.bt2
├── host.fasta.4.bt2
├── host.fasta.rev.1.bt2
├── host.fasta.rev.2.bt2
└── NC_001422.fasta

adapter

mkdir -p reference/adpater/
./
├── NexteraPE-PE.fa
├── TruSeq2-PE.fa
├── TruSeq2-SE.fa
├── TruSeq3-PE-2.fa
├── TruSeq3-PE.fa
└── TruSeq3-SE.fa
Download files from Trimmomatic(http://www.usadellab.org/cms/index.php?page=trimmomatic)

ResFinder

mkdir reference/ResFinder
cd reference/ResFinder
git clone https://[email protected]/genomicepidemiology/resfinder_db.git
python3 INSTALL.py

ResFinder/
└── resfinder_db
    ├── all.comp.b
    ├── all.length.b
    ├── all.name
    ├── all.seq.b
    ├── aminoglycoside.comp.b
    ├── aminoglycoside.fsa
    ├── aminoglycoside.length.b
    ├── aminoglycoside.name
    ├── aminoglycoside.seq.b
    ├── antibiotic_classes.txt
    ├── beta-lactam.comp.b
    ├── beta-lactam.fsa
    ├── beta-lactam.length.b
    ├── beta-lactam.name
    ├── beta-lactam.seq.b
    ├── CHECK-entries.sh
    ├── colistin.comp.b
    ├── colistin.fsa
    ├── colistin.length.b
    ├── colistin.name
    ├── colistin.seq.b
    ├── config
    ├── disinfectant.comp.b
    ├── disinfectant.fsa
    ├── disinfectant.length.b
    ├── disinfectant.name
    ├── disinfectant.seq.b
    ├── fosfomycin.comp.b
    ├── fosfomycin.fsa
    ├── fosfomycin.length.b
    ├── fosfomycin.name
    ├── fosfomycin.seq.b
    ├── fusidicacid.comp.b
    ├── fusidicacid.fsa
    ├── fusidicacid.length.b
    ├── fusidicacid.name
    ├── fusidicacid.seq.b
    ├── glycopeptide.comp.b
    ├── glycopeptide.fsa
    ├── glycopeptide.length.b
    ├── glycopeptide.name
    ├── glycopeptide.seq.b
    ├── history.txt
    ├── INSTALL.py
    ├── macrolide.comp.b
    ├── macrolide.fsa
    ├── macrolide.length.b
    ├── macrolide.name
    ├── macrolide.seq.b
    ├── nitroimidazole.comp.b
    ├── nitroimidazole.fsa
    ├── nitroimidazole.length.b
    ├── nitroimidazole.name
    ├── nitroimidazole.seq.b
    ├── notes.txt
    ├── oxazolidinone.comp.b
    ├── oxazolidinone.fsa
    ├── oxazolidinone.length.b
    ├── oxazolidinone.name
    ├── oxazolidinone.seq.b
    ├── phenicol.comp.b
    ├── phenicol.fsa
    ├── phenicol.length.b
    ├── phenicol.name
    ├── phenicol.seq.b
    ├── phenotype_panels.txt
    ├── phenotypes.txt
    ├── pseudomonicacid.comp.b
    ├── pseudomonicacid.fsa
    ├── pseudomonicacid.length.b
    ├── pseudomonicacid.name
    ├── pseudomonicacid.seq.b
    ├── quinolone.comp.b
    ├── quinolone.fsa
    ├── quinolone.length.b
    ├── quinolone.name
    ├── quinolone.seq.b
    ├── README.md
    ├── rifampicin.comp.b
    ├── rifampicin.fsa
    ├── rifampicin.length.b
    ├── rifampicin.name
    ├── rifampicin.seq.b
    ├── sulphonamide.comp.b
    ├── sulphonamide.fsa
    ├── sulphonamide.length.b
    ├── sulphonamide.name
    ├── sulphonamide.seq.b
    ├── tetracycline.comp.b
    ├── tetracycline.fsa
    ├── tetracycline.length.b
    ├── tetracycline.name
    ├── tetracycline.seq.b
    ├── trimethoprim.comp.b
    ├── trimethoprim.fsa
    ├── trimethoprim.length.b
    ├── trimethoprim.name
    └── trimethoprim.seq.b

diamond

mkdir reference/diamond
wget https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz
wget https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
tar xzvf taxdump.tar.gz
wget https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz
diamond makedb --in nr.gz -d reference --taxonmap prot.accession2taxid.gz --taxonnodes nodes.dmp --taxonnames names.dmp

diamond/reference.dmnd

megan6

https://software-ab.informatik.uni-tuebingen.de/download/megan6/welcome.html
# download mapping file:
mkdir reference/MEGAN
wget https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-map-Feb2022.db.zip
gunzip megan-map-Feb2022.db.zip

MEGAN/
├── megan-map-Feb2022.db
└── megan-map-Feb2022.db.zip

VFDB

mkdir reference/VFDB
wget http://www.mgc.ac.cn/VFs/Down/VFDB_setB_nt.fas.gz
wget http://www.mgc.ac.cn/VFs/Down/VFDB_setB_pro.fas.gz
makeblastdb -in VFDB_setB_nt.fas -dbtype nucl -out VFDB_setB_nt.fas
makeblastdb -in VFDB_setB_pro.fas -dbtype prot -out VFDB_setB_pro.fas

VFDB/
├── VFDB_setB_nt.fas
├── VFDB_setB_nt.fas.nhr
├── VFDB_setB_nt.fas.nin
├── VFDB_setB_nt.fas.nsq
├── VFDB_setB_pro.fas
├── VFDB_setB_pro.fas.phr
├── VFDB_setB_pro.fas.pin
└── VFDB_setB_pro.fas.psq

taxonomy

mkdir -p /reference/taxonomy/accession2taxid
cd /reference/taxonomy/accession2taxid
wget https://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz
wget https://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/nucl_wgs.accession2taxid.gz
wget https://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz
wget https://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/dead_wgs.accession2taxid.gz
wget https://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/dead_prot.accession2taxid.gz
wget https://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/dead_nucl.accession2taxid.gz
/software/KronaTools-2.8.1/updateAccessions.sh --only-build /reference/taxonomy/
wget https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
/software/KronaTools-2.8.1/updateTaxonomy.sh --only-build /reference/taxonomy/