/genomes

Primary LanguagePerlMIT LicenseMIT

Genomes

date

The date of executing nwr download is Wed May 31 20:14:22 CST 2023

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

Packages managed by Homebrew

brew install hmmer
brew install brewsci/bio/easel
brew install mafft
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 datamash
brew install miller
brew install wang-q/tap/tsv-utils
brew install wang-q/tap/faops

brew install librsvg
brew install jq
brew install pup

# 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

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 |
    mlr --itsv --omd cat
Ranks: higher taxa genus species lower taxa total
Archaea 593 257 867 0 1,717
Bacteria 5,783 4,973 24,503 950 36,209
Eukaryota 66,566 98,103 512,437 36,398 713,504
Fungi 5,970 7,405 55,346 1,562 70,283
Metazoa 48,238 69,901 268,271 18,162 404,572
Viridiplantae 8,413 16,876 174,241 16,302 215,832
Viruses 2,045 2,584 7,178 65 11,872
All taxa 75,018 105,919 544,971 37,413 763,321

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

Eukaryote groups