If you found this software useful to your research please cite as follows:
Garber, A. I., Armbruster, C. R., Lee, S. E., Cooper, V. S., Bomberger, J. M., & McAllister, S. M. (2021). SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs. In bioRxiv (p. 2021.07.17.452725). https://doi.org/10.1101/2021.07.17.452725
Please also cite the various dependencies used by spray-and-pray: DIAMOND, Prodigal, Metabat2, and Biopython
Provide either raw contigs or ORFs (amino acid) in FASTA format. A reference protein dataset also needs to be provided. Ideally, this should be NCBI's RefSeq or nr database from NCBI, which can be downloaded via (or follow the install instructions):
wget ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nr.gz
This program will then DIAMOND BLAST each ORF against the reference database (This takes about 30 minutes for a typical bacteria genome of ~4Mbp).
The program will then output a file in CSV format summarizing the dominant taxanomic groups matched to each contig. This allows the user to visually inspect the data, seeing what the closest taxonomic group to each contig is. Additionally, the user can specify a set of criteria (e.g. GC-content, read coverage, coding density, closest taxonomic hits) to re-write the provided contigs into a new FASTA file.
git clone https://github.com/Arkadiy-Garber/SprayNPray.git
cd SprayNPray
bash setup.sh
bash dlDB.sh /path/to/preferred/directory/for/db
conda activate sprayandpray
Please also place spray-and-pray.py into the PATH variable: e.g. ~/bin/SprayNPray. You can update the PATH variable in a file called '.bash_profile' or '.profile' in your home directory.
Do not worry about the dependencies after conda installation. Just enter conda deactivate when finished using the program.
git clone https://github.com/Arkadiy-Garber/SprayNPray.git
export PATH=$PATH:$(pwd)
(be sure to put spray-and-pray.py into your $PATH in your bash profile)
bash testRun.sh
spray-and-pray.py -g genomeContigs.fa -out genomeContigs -ref /path/to/nr/nr.faa
spray-and-pray.py -a pseudomonas_crude.fa -out pseudomonas_clean.fa -Genus Pseudomonas -species aeruginosa -perc 50 --fa -ref /path/to/nr/nr.faa
In the above command, we require that at least 50% of contig's genes have a top DIAMOND hit to Pseudomonas aruginosa. Contigs matching these parameters will be written to a new FASTA file: pseudomonas_clean.fa
spray-and-pray.py -a M_hirsutus_assembly.fa -out endosymbionts.fa -cd 0.5 -L 1000000 -perc 50 --fa -ref /path/to/nr/nr.faa -Domain Bacteria
In the above comomand, we require a gene density of 0.5 genes per kb, maximum length of 1 Mb, top DIAMOND hit to be to a bacterial gene, and that at least 50% of the contig's genes to be of bacterial origin to be written to endosymbionts.fa
spray-and-pray.py -a P_citri.fa -out putative_hgts.csv --hgt -ref /path/to/nr/nr.faa
