Find your sequenced isolate a compatable reference genome based on location, interests, and mash distance.
This repository contains the pipeline to identity a suitable reference isolate based on comparing a mini assembly to a set of complete genomes via mash. For more information on using this with riboSeed, see this page on choosing reference genomes.
plentyofbugs requires
- skesa (or spades)
- seqtk
- mash
conda create pob skesa seqtk mash
conda activate pob
pip install plentyofbugs
plentyofbugs -h
The data in the test_data directory was gathered using the test_data/get_data.sh script. It consists of 19 plasmids from E coli, and a test plasmid from which reads were generated using ART. https://www.niehs.nih.gov/research/resources/software/biostatistics/art/. The contigs in this diretory were made with SKESA.
# running with raw reads
plentyofbugs -g ./test_data/plasmids/ -f ./test_data/test_reads1.fq -o tmp
# running with an assembly instead of raw reads
plentyofbugs -g ./test_data/plasmids/ --assembly ./test_data/contigs.fasta -o tmp
# running on a new cast of E coli genomes to compare to, downloading the required genomes on the way
plentyofbugs -g ./new_comparison_e_coli/ -n 5 --assembly ./test_data/contigs.fasta -o tmp --genus_species "Escherichia coli"
Plentyofbugs includes the genomes-getter as a standalone script: get_n_genomes.
get_n_genomes -o "Escherichia coli" -g tmpnewgenomes -n 4
NOTE: To run the legacy version that used pyani, run a version older than 0.87 with Docker or singularity -- it will save yourself a lot of trouble!
docker run --rm -t -v ${PWD}:/data/ nickp60/plentyofbugs:0.97 -f /data/test_reads1.fq --genus_species "Escherichia coli" -n 5 -o /data/results/
which is
docker run --rm -t -v <current directory>:/data/ nickp60/plentyofbugs:0.97 -f /data/<name of F reads file> --genus_species "<bug of interest>" -n <max number of strains to compare with> -o /data/<name for output folder>/
singularity pull docker://nickp60/plentyofbugs:0.97
plentyofbugs:0.92.sing -f ./test_reads1.fq --genus_species "Escherichia coli" -n 5 -o ./results/
- Runs a mini assembly with skesa or SPAdes
- Identify which complete genomes are available for the genus and species
- optional Subset number of complete genomes
- Download reference genomes
- Indexes/sketches genomes
- Calculate the Mash distance/ANI of the mini assembly to the database of reference strains
- Report the closest reference genome and the distance/ANI