$ taxon-utils
Usage: taxon-utils <command> <arguments>
Version: 0.0.1-r1
Command:
translate translate the taxon_id map to lineage.
lineage translate the taxon_id map to full lineage.
name translate the taxon_id map to name.
lca perform lca for given taxon match per query.
bin bin reads for specify level. default: [species] .
clade get clade taxon id from NCBI taxonomy tree.
filter filter the entries with specified taxonIds.
Licenced:
(c) 2018-2020 - LEI ZHANG
Logic Informatics Co.,Ltd.
zhanglei@logicinformatics.com
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