taxon-utils: utils for NCBI taxonomy manipulation
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
README.md
ncbi.map.gz
species_assign
taxon-db
taxon-translate

README.md

taxon-utils

taxon-utils: utils for NCBI taxonomy manipulation

species_assign

Example:

wget https://zenodo.org/record/824551/files/silva_species_assignment_v128.fa.gz
gunzip silva_species_assignment_v128.fa.gz
grep ">" silva_species_assignment_v128.fa | sed 's/>//' | cut -f1,2,3 -d ' ' >silva_species_assignment_v128.map

bowtie  -f -v 0 -a silva_species_assignment_v128 example_seqs.fa 2>/dev/null | species_assign  silva_species_assignment_v128.map