This tool is designed to assign species to a Klebsiella assembly. However, unlike other tools, like Kleborate which assign a single species, this tool 'paints' each region with a species, allowing it to detect and characterise cross-species hybrids.
BLAST+ commands must be available on the command line (specifically the commands makeblastdb, blastn and tblastn). BLAST+ can usually be easily installed using a package manager such as Homebrew (on Mac) or apt-get (on Ubuntu and related Linux distributions).
You'll need reference genome assemblies for each Klebsiella species: pneumoniae, quasipneumoniae_subsp_quasipneumoniae, quasipneumoniae_subsp_similipneumoniae, variicola, quasivariicola, oxytoca, michiganensis, grimontii and aerogenes. Put these in a directory and make sure that the species name (exactly as shown here) is in the path or filename. It's better to have a good variety of genomes from each species, as this will better capture the pan genome. However, more genomes will cause the tool to run slower, so you may need to strike a balance. Also, ensure that no hybrids are in your reference set, e.g. a genome which is a blend of pneumoniae and variicola.
This tool is a single Python 3 script with no third-party dependencies. It will run without any installation:
git clone https://github.com/rrwick/Klebsiella-assembly-species
Klebsiella-assembly-species/klebsiella_assembly_species.py --help
If you want, you can copy the it to somewhere in your PATH for easy usage:
cp Klebsiella-assembly-species/klebsiella_assembly_species.py ~/.local/bin
klebsiella_assembly_species.py --help
Test one assembly:
klebsiella_assembly_species.py --reference_dir references klebs_assembly.fasta
Test many assemblies:
klebsiella_assembly_species.py --reference_dir references klebs_assemblies/*.fasta
Save blocks for plotting in R:
klebsiella_assembly_species.py --reference_dir references --save_blocks block_dir klebs_assemblies/*.fasta
usage: klebsiella_assembly_species.py [-h] [--hit_length HIT_LENGTH]
[--hit_id HIT_ID] [--min_diff MIN_DIFF]
[--min_block_size MIN_BLOCK_SIZE]
[--reference_dir REFERENCE_DIR]
[--save_blocks SAVE_BLOCKS]
[--save_match_vals SAVE_MATCH_VALS]
queries [queries ...]
Klebsiella species assembly checker
positional arguments:
queries FASTA file(s) of assembly to check
optional arguments:
-h, --help show this help message and exit
--hit_length HIT_LENGTH
BLAST hits shorter than this will be ignored (default:
100)
--hit_id HIT_ID BLAST hits with lower identity than this will be
ignored (default: 98.0)
--min_diff MIN_DIFF Bases will not be assigned to a species if they have
less than this much difference between the best and
second-best species (default: 0.5)
--min_block_size MIN_BLOCK_SIZE
Blocks smaller than this size will be filtered out
(default: 10000)
--reference_dir REFERENCE_DIR
Where to find the reference genomes (default: same
directory as script)
--save_blocks SAVE_BLOCKS
Saves blocks files for each query to this directory
(default: do not save blocks)
--save_match_vals SAVE_MATCH_VALS
Saves blocks files for each query to this directory
(default: do not save match values)