---
# System prepended metadata

title: Ganon read-based taxonomy classification
tags: [cov-irt]

---

---
tags: cov-irt
---

# Ganon read-based taxonomy classification

## Installation
Creating and installing in a new conda environment:

```bash
conda create -y -n ganon -c conda-forge -c bioconda -c defaults ganon=0.2.3 genome_updater=0.2.2
conda activate ganon
```

## Getting pre-built database
Will add when uploaded somewhere


## How ref db was built on 29-July-2020

**Not needed to run, just here for documentation**
```bash
# genome_updater.sh -g archaea,bacteria,human,viral,fungi -d refseq -l "Complete Genome" -f genomic.fna.gz,assembly_report.txt -o refseq-complete-genomes-arc-bac-human-viral-fungi -b v1 -a -m -u -r -p -t 42
# ganon build --db-prefix ganon-complete-genomes-arc-bac-human-viral-fungi --input-directory refseq-complete-genomes-arc-bac-human-viral-fungi/v1/files/ --input-extension "_genomic.fna.gz" -t 42
```

## Building new db so has sars-cov-2

Doing on `astrobio@129.114.17.158`

```bash
genome_updater.sh -g archaea,bacteria,human,viral,fungi -d refseq -l "Complete Genome" -f genomic.fna.gz,assembly_report.txt -o ganon-db-ref -b v1 -a -m -u -r -p -t 42
ganon build --db-prefix ganon-db-ref --input-directory ganon-db-ref/v1/files/ --input-extension "_genomic.fna.gz" -t 42
```


## Example run

Downloading one of our samples (CRR125950):

```bash
curl -L -o CRR125950_filtered_1_reads_trim25_1.fq.gz https://osf.io/hg7p4/download
```

Running classification:

```bash
ganon classify -d ganon-db-ref \
               -r CRR125950_filtered_1_reads_trim25_1.fq.gz \
               -t 40 -o CRR125950_filtered_1_reads_trim25_1-ganon-out 
```


We can filter/modify the output from that with the ganon report command, here's one example:

```bash
ganon report -d ganon-db-ref \
             --rep-file CRR125950_filtered_1_reads_trim25_1-ganon-out.rep --ranks species \
             --output-report CRR125950_filtered_1_reads_trim25_1-ganon-out-species.tre
```