Enveomics collection

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

• Ruby >= 2.0.

§ 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.

* Mandatory.