Ganon read-based taxonomy classification

Installation

Creating and installing in a new conda environment:

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

# 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

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):

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

Running classification:

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:

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