Genomes

• Genomes
  • date
  • Software
    • Install nwr and initiate local databases
    • Packages managed by Homebrew
    • Other Packages
  • Strain info
    • NCBI statistics
  • Download all valid Bacteria and Archaea genomes
  • Prokaryote groups
  • Eukaryote groups

date

The date of executing nwr download is Fri Nov 15 15:51:01 CST 2024

Software

Install nwr and initiate local databases

brew install wang-q/tap/nwr # 0.5.4 or above
brew install sqlite         # 3.34 or above
#brew link sqlite --force

nwr download
nwr txdb

nwr ardb
nwr ardb --genbank

cd $HOME/.nwr
tar cvfz ncbi.$(date +"%Y%m%d").tar.gz \
    taxdump.tar.gz \
    taxdump.tar.gz.md5 \
    assembly_summary_genbank.txt \
    assembly_summary_refseq.txt

rm \
    taxdump.tar.gz \
    taxdump.tar.gz.md5 \
    assembly_summary_genbank.txt \
    assembly_summary_refseq.txt

Packages managed by Homebrew

brew install hmmer
brew install brewsci/bio/easel
brew install mafft
brew install samtools
brew install brewsci/bio/muscle
brew install brewsci/bio/fasttree
brew install brewsci/bio/iqtree2
brew install brewsci/bio/newick-utils
brew install brewsci/bio/trimal
brew install brewsci/bio/mash
brew install mmseqs2

brew install datamash
brew install wang-q/tap/tsv-utils
brew install wang-q/tap/faops
brew install wang-q/tap/hnsm

cargo install fd-find
cargo install qsv --locked --features feature_capable,apply,lens,luau,polars

brew install jq
brew install pup
brew install pigz

curl -LO https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-AVX2-Linux.tar.gz

curl -LO https://github.com/soedinglab/spacedust/releases/download/1-babc6f8/spacedust-linux-avx2.tar.gz

curl --proto '=https' --tlsv1.2 -fsSL https://drop-sh.fullyjustified.net | sh
mv tectonic ~/bin/

# dN/dS
brew install brewsci/bio/clustal-w
brew install brewsci/bio/paml

cpanm Bio::Tools::Run::Alignment::Clustalw
cpanm https://github.com/wang-q/Bio-Tools-Phylo-PAML.git

Other Packages

• Pangenome
  • PPanGGOLiN is used in this project. Installation steps can be found here.

Strain info

• Bacteria
• Archaea
• Fungi
• Oomycota

NCBI statistics

curl -L "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=statistics&uncultured=hide&unspecified=hide" |
    pup 'table[bgcolor=#CCCCFF] tr td text{}' |
    grep '\S' |
    paste -d $'\t' - - - - - - |
    head -n 9 |
    rgr md stdin --right 2-6

Ranks:	higher taxa	genus	species	lower taxa	total
Archaea	742	314	1,046	0	2,102
Bacteria	7,192	5,435	27,084	972	40,683
Eukaryota	71,173	102,113	551,181	39,017	763,484
Fungi	6,810	7,842	61,751	1,619	78,022
Metazoa	51,179	73,101	287,542	19,570	431,392
Viridiplantae	8,825	17,071	186,365	17,424	229,685
Viruses	2,328	2,853	5,815	963	11,959
All taxa	81,466	110,716	585,112	40,952	818,246

Download all valid Bacteria and Archaea genomes

• Trichoderma is a good example of familiarizing yourself with the processing steps.

• Bacteria: All genomes of Bacteria and Archaea, species by species

• Fungi: All genomes of Fungi, species by species

Prokaryote groups

• Pseudomonas
• MTBC
• Tenericutes

Eukaryote groups

• Trichoderma
• Protistis