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README.md

taxon-utils: utils for taxonomy manipulation

interface

$ 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

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

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taxon-utils: utils for NCBI taxonomy manipulation

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