Enveomics collection

A toolbox for microbial genomics and metagenomics

BlastTab.taxid2taxrank.pl

Takes a BLAST with NCBI Taxonomy IDs as subjects and replaces them by names at a given taxonomic rank.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

§ Usage

BlastTab.taxid2taxrank.pl in_file in_file in_file string [opts] > out_file

§ Arguments

tax_blast.txt*
 in_file  BLAST output, where subject IDs are NCBI Taxonomy IDs.
nodes.dmp*
 in_file  Nodes file from NCBI Taxonomy.
names.dmp*
 in_file  Names file from NCBI Taxonomy.
rank*
 string  The rank to be reported. All the reported nodes will have the same rank. To see supported values, run: `cut -f 5 nodes.dmp | sort -u`.
Best-hit
 select  Should it take into account the best hit per query only? This is: should it filter by best-hit?
taxrank_list.txt*
 out_file  BLAST-like output, where subject IDs are Taxonomy names.
* Mandatory.