date
- Software
- Strain info
- Download all valid Bacteria and Archaea genomes
- Prokaryote groups
- Eukaryote groups
The date of executing nwr download
is Wed May 31 20:14:22 CST 2023
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
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
- Pangenome
PPanGGOLiN
is used in this project. Installation steps can be found here.
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 |
-
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
- Pseudomonas
- MTBC
- Tenericutes