Taxonomy.silva2ncbi.rb
Re-formats Silva taxonomy into NCBI-like taxonomy dump files.
See source code, Artistic license 2.0.
§ References
Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.
§ Requirements
§ Usage
Taxonomy.silva2ncbi.rb --silvaranks in_file --silvaref in_file [opts]
§ Arguments
- Silvaranks*
--silvaranks in_file
Input Silva ranks file (e.g., tax_ranks_ssu_115.txt).- Silvaref*
--silvaref in_file
Input Silva ref alignment file (e.g., SSURef_NR99_115_tax_silva_full_align_trunc.fasta).- Patch
--patch in_file
If passed, it replaces the paths specified in the patch.- Seqinfo
--seqinfo out_file
If passed, it creates a CSV seq-info file compatible with taxtastic.- Taxfile
--taxfile out_file
If passed, it creates a simple TSV taxonomy file.- Ncbi
--ncbi out_dir
If passed, output folder for the NCBI dump files (e.g., taxdmp).- Warns
--warns
Verbously display warnings.