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# argNorm | ||
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[![Python package](https://github.com/BigDataBiology/argNorm/actions/workflows/python-package.yml/badge.svg)](https://github.com/BigDataBiology/argNorm/actions/workflows/python-package.yml) | ||
[![Downloads](https://pepy.tech/badge/argNorm)](https://pepy.tech/project/argNorm) | ||
![](https://img.shields.io/badge/status-alpha-red?style=flat) | ||
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Antibiotic resistance gene (ARG) normalization by mapping to the [antibiotic resistance ontology (ARO)](https://obofoundry.org/ontology/aro.html) by CARD. | ||
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Right now, many tools exist for annotating ARGs in genomes and metagenomes. | ||
However, each tool will output in its own format. | ||
The [hAMRonization](https://github.com/pha4ge/hAMRonization) package can normalize file formats, but each tool will use different names/identifiers (_e.g._, `TetA` or `TETA` or `tet(A)` or `tet-A` are all different ways to spell the same gene name). | ||
For a small number of isolate genomes, a human user can still quickly evaluate the outputs. | ||
However, for metagenomics, especially for large-scale projects, this becomes infeasible. | ||
Thus, `argNorm` normalizes the _output vocabulary_ of these tools by mapping all tools to the same ontology (ARO). | ||
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This is a beta-quality implementation (subject to changes and some bugs may remain), but you're welcomed to try it and provide feedback. | ||
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We welcome your feedback on the [Issues Page](https://github.com/BigDataBiology/argNorm/issues). | ||
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## Supported tools | ||
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Note that CARD RGI already uses ARO, thus there is no need to use argNorm. | ||
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- [x] [DeepARG](https://bench.cs.vt.edu/deeparg) (v1.0.2) | ||
- [x] [ARGs-OAP](https://galaxyproject.org/use/args-oap/) (v2.3) | ||
- [x] [ABRicate](https://github.com/tseemann/abricate) (v1.0.1) with NCBI (v3.6), ResFinder (v4.1.11), MEGARes (v2.0), ARG-ANNOT (v5) | ||
- [x] [ResFinder](https://bitbucket.org/genomicepidemiology/resfinder/src/master/) (v4.0) | ||
- [x] [AMRFinderPlus](https://github.com/ncbi/amr) (v3.10.30) | ||
<!-- Hamronized output | ||
- [x] [deeparg](https://bitbucket.org/gusphdproj/deeparg-largerepo/src/master/database/v2/features.fasta) | ||
- [x] [sarg](https://smile.hku.hk/SARGs/static/images/Ublastx_stageone2.3.tar.gz) | ||
- [x] [ncbi](https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/AMRProt) | ||
- [x] [argannot](https://github.com/tseemann/abricate/tree/master/db/argannot) | ||
- [x] [megares](https://github.com/tseemann/abricate/tree/master/db/megares) | ||
- [x] [resfinder](https://bitbucket.org/genomicepidemiology/resfinder_db) --> | ||
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<!-- Raw output | ||
- [x] [deeparg](https://bitbucket.org/gusphdproj/deeparg-largerepo/src/master/database/v2/features.fasta) | ||
- [ ] [sarg](https://smile.hku.hk/SARGs/static/images/Ublastx_stageone2.3.tar.gz) | ||
- [x] [ncbi](https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/AMRProt) | ||
- [x] [argannot](https://github.com/tseemann/abricate/tree/master/db/argannot) | ||
- [x] [megares](https://github.com/tseemann/abricate/tree/master/db/megares) | ||
- [ ] [resfinder](https://bitbucket.org/genomicepidemiology/resfinder_db) --> | ||
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## Installation | ||
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```bash | ||
pip install argnorm | ||
``` | ||
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## Basic usage | ||
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Use `argnorm -h` to see available options. | ||
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```bash | ||
argnorm [tool] -i [original_annotation.tsv] -o [annotation_result_with_aro.tsv] | ||
``` | ||
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## Examples | ||
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```bash | ||
argnorm argsoap --mode reads -i examples/raw/args-oap.sarg.reads.tsv -o tmp | ||
argnorm argsoap --mode reads -i examples/hamronized/args-oap.sarg.reads.tsv -o tmp --hamronized | ||
argnorm argsoap --mode orfs -i examples/raw/args-oap.sarg.orfs.tsv -o tmp | ||
argnorm argsoap --mode orfs -i examples/hamronized/args-oap.sarg.orfs.tsv -o tmp --hamronized | ||
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argnorm deeparg -i examples/raw/deeparg.deeparg.orfs.tsv -o tmp | ||
argnorm deeparg -i examples/hamronized/deeparg.deeparg.orfs.tsv -o tmp --hamronized | ||
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argnorm abricate --db ncbi -i examples/raw/abricate.ncbi.tsv -o tmp | ||
argnorm abricate --db megares -i examples/raw/abricate.megares.tsv -o tmp | ||
argnorm abricate --db argannot -i examples/raw/abricate.argannot.tsv -o tmp | ||
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argnorm abricate --db ncbi -i examples/hamronized/abricate.ncbi.tsv -o tmp --hamronized | ||
argnorm abricate --db megares -i examples/hamronized/abricate.megares.tsv -o tmp --hamronized | ||
argnorm abricate --db argannot -i examples/hamronized/abricate.argannot.tsv -o tmp --hamronized | ||
argnorm abricate --db resfinder -i examples/hamronized/abricate.resfinder.tsv -o tmp --hamronized | ||
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argnorm resfinder -i examples/raw/resfinder.resfinder.orfs.tsv -o outputs/raw/resfinder.resfinder.orfs.tsv | ||
argnorm resfinder -i examples/raw/resfinder.resfinder.reads.tsv -o outputs/raw/resfinder.resfinder.reads.tsv | ||
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argnorm amrfinderplus -i examples/raw/amrfinderplus.ncbi.orfs.tsv -o outputs/raw/amrfinderplus.ncbi.orfs.tsv | ||
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``` |
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site_name: "argNorm: Normalize ARG annotations to ARO" | ||
repo_url: "https://github.com/BigDataBiology/argNorm" | ||
repo_name: "GitHub" | ||
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theme: | ||
name: readthedocs | ||
highlightjs: true | ||
html_show_sourcelink: false | ||
prev_next_buttons_location: both | ||
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nav: | ||
- 'argNorm': index.md | ||
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