abritamr 1.0.20b0
Running AMRFinderPlus for MDU
Requires Python: <4,>=3.9

<figure><img src="documentation/abriTAMR_logo.jpg"></figure>

**_logo by Charlie Higgs (PhD candidate)_**

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**_Taming the AMR beast_**

abriTAMR is an AMR gene detection pipeline that runs AMRFinderPlus on a single (or  list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.

_abriTAMR is accredited by NATA for use in reporting the presence of reportable AMR genes in Victoria Australia._

* Acquired resistance mechanims in the form of point mutations (restricted to subset of species)
* Streamlined output.
* Presence of virulence factors

## Install

### Conda

abritAMR is best installed with `conda` as described below (~2 minutes on laptop)


```
conda create -n abritamr -c bioconda abritamr
conda activate abritamr
```

### A note on dependencies

abriTAMR requires [AMRFinder Plus](https://github.com/ncbi/amr), this can be installed separately with `conda` if required. 

abriTAMR comes packaged with a version of the  AMRFinder DB consistent with current NATA accreditation. If you would like to use another DB please download it using `amrfinder -U` and use the `-d` flag to point to your database.

Current version of AMRFinder Plus compatible with abritAMR 3.10.42 (tested on versions down to 3.10.16)



## Command-line tool

```
abritamr run --help


optional arguments:
  -h, --help            show this help message and exit
  --contigs CONTIGS, -c CONTIGS
                        Tab-delimited file with sample ID as column 1 and path to assemblies as column 2 OR path to a contig
                        file (used if only doing a single sample - should provide value for -pfx). (default: )
  --prefix PREFIX, -px PREFIX
                        If running on a single sample, please provide a prefix for output directory (default: abritamr)
  --jobs JOBS, -j JOBS  Number of AMR finder jobs to run in parallel. (default: 16)
  --identity IDENTITY, -i IDENTITY
                        Set the minimum identity of matches with amrfinder (0 - 1.0). Defaults to amrfinder preset, which is 0.9
                        unless a curated threshold is present for the gene. (default: )
  --amrfinder_db AMRFINDER_DB, -d AMRFINDER_DB
                        Path to amrfinder DB to use (default:
                        /<path_to_installation>/abritamr/abritamr/db/amrfinderplus/data/2021-09-30.1)
  --species {Neisseria,Clostridioides_difficile,Acinetobacter_baumannii,Campylobacter,Enterococcus_faecalis,Enterococcus_faecium,Escherichia,Klebsiella,Salmonella,Staphylococcus_aureus,Staphylococcus_pseudintermedius,Streptococcus_agalactiae,Streptococcus_pneumoniae,Streptococcus_pyogenes}, -sp {Neisseria,Clostridioides_difficile,Acinetobacter_baumannii,Campylobacter,Enterococcus_faecalis,Enterococcus_faecium,Escherichia,Klebsiella,Salmonella,Staphylococcus_aureus,Staphylococcus_pseudintermedius,Streptococcus_agalactiae,Streptococcus_pneumoniae,Streptococcus_pyogenes}
                        Set if you would like to use point mutations, please provide a valid species. (default: )
```

You can also run abriTAMR in `report` mode, this will output a spreadsheet which is based on reportable/not-reportable requirements in Victoria. You will need to supply a quality control file (comma separated) (`-q`), with the following columns:

* ISOLATE
* SPECIES_EXP (the species that was expected)
* SPECIES_OBS (the species that was observed during the quality control analysis)
* TEST_QC (PASS or FAIL)

`--sop` refers to the type of collation and reporting pipeline
* general
  * standard reporting structure for aquired genes, output as reportable and non-reportable
* plus
  * Inferred AST based on validation undertaken at MDU

```
abritamr report --help

optional arguments:
  -h, --help            show this help message and exit
  --qc QC, -q QC        Name of checked MDU QC file. (default: )
  --runid RUNID, -r RUNID
                        MDU RunID (default: Run ID)
  --matches MATCHES, -m MATCHES
                        Path to matches, concatentated output of abritamr (default: summary_matches.txt)
  --partials PARTIALS, -p PARTIALS
                        Path to partial matches, concatentated output of abritamr (default: summary_partials.txt)
  --sop {general,plus}  The MDU pipeline for reporting results. (default: general)
```

## Output

### `abritAMR run` 

Outputs 4 summary files and retains the raw AMRFinderPlus output for each sequence input.

1. `amrfinder.out` raw output from AMRFinder plus (per sequence). For more information please see AMRFinderPlus help [here](https://github.com/ncbi/amr/wiki/Interpreting-results) 

2.  `summary_matches.txt` 
  * Tab-delimited file, with a row per sequence, and columns representing functional drug classes 
  * Only genes recovered from sequence which have >90% coverage of the gene reported and greater than the desired identity threshold (default 90%). 
    
    I. Genes annotated with `*` indicate >90% coverage and > identity threshold < 100% identity.
    
    II. No further annotation indicates that the gene recovered exhibits 100% coverage and 100% identity to a gene in the gene catalog.
    
    III. Point mutations detected (if `--species` supplied) will also be present in this file in the form of `gene_AAchange`.

3. `summary_partials.txt`
  * Tab-delimited file, with a row per sequence, and columns representing functional drug classes 
  * Genes recovered from sequence which have >50% but <90% coverage of the gene reported and greater than the desired identity threshold (default 90%). 

4. `summary_virulence.txt`
  * Tab-delimited file, with a row per sequence, and columns representing AMRFinderPlus virulence gene classification
  * Genes recovered from sequence which have >50% coverage of the gene reported and greater than the desired identity threshold (default 90%). 

      * Genes recovered with >50% but <90% coverage of a gene in the gene catalog will be annotated with `^`.
      * Genes annotated with `*` indicate >90% coverage and > identity threshold < 100% identity.

4. `abritamr.txt`
  * Tab-delimited file, combining `summary_matches.txt`, `summary_partials.txt`, `summary_virulence.txt` with a row per sequence, and columns representing AMRFinderPlus virulence gene classification and/or functional drug classes.
  * Genes recovered from sequence which have >50% coverage of the gene reported and greater than the desired identity threshold (default 90%). 

      * Genes recovered with >50% but <90% coverage of a gene in the gene catalog will be annotated with `^`.
      * Genes annotated with `*` indicate >90% coverage and > identity threshold < 100% identity.

### `abritamr report` 

will output spreadsheets `general_runid.xlsx` (NATA accredited) or `plus_runid.xlsx` (validated - not yet accredited) depending upon the sop chosen.

* `general_rundid.xlsx` has two tabs, one for matches and one for partials (corresponding to genes reported in the `summary_matches.txt` and `summary_partials.txt`). Each tab has 7 columns 

| Column | Interpretation |
|:---: | :---: |
| MDU sample ID | Sample ID |
|Item code | suffix (MDU specific) |
| Resistance genes (alleles) detected | genes detected that are reportable (based on species and drug classification)|
| Resistance genes (alleles) det (non-rpt) | other genes detected that are not not reportable for the species detected.
| Species_obs | Species observed (supplied in input file) |
| Species_exp | Species expected (supplied in input file) |
| db_version | Version of the AMRFinderPlus DB used |

* `plus_runid.xlsx` output is a spreadsheet with the different drug resistance mechanims and the corresponding interpretation (based on validation of genotype and phenotype) for drug-classes relevant to reporting of anti-microbial resistance in _Salmonella enterica_ (other species will be added as validation of genotype vs phenotype is performed).

* Ampicillin
* Cefotaxime (ESBL) 
* Cefotaxime (AmpC)
* Tetracycline
* Gentamicin
* Kanamycin
* Streptomycin
* Sulfathiazole
* Trimethoprim
* Trim-Sulpha
* Chloramphenicol 
* Ciprofloxacin
* Meropenem 
* Azithromycin
* Aminoglycosides (RMT)
* Colistin