calculate pair-wise allelic distances from cgMLST implements chewBBACAs
Project description
COREugate - A pipeline for cgMLST
From contigs to cgMLST profile and SLC.
COREugate has had a small facelift!! Under the hood we are now using NextFlow as our pipeline engine and have introduced some additional functionality for clustering the profiles.
- PrepSchema (if necessary) and Call alleles using chewBBACA.
- Combine profiles and statisitics for the whole dataset.
- Calculate pairwise allelic distances (missing data is ignored)
- Perform SLC to group related profiles, based on user supplied thresholds.
Dependencies
Python >=3.7
Biopython >=1.70
Nextflow >=20.10
chewBBACA >=2.6
NextFlow
Ensure that you have NextFlow installed. Detailed instructions can be found here
chewBBACA
chewBBACA is used here to prepare the schema, by selecting exemplar alleles for comparison and to call allele profiles. More information about chewBBACA and how it is works can be found here. COREugate can use a singularity version of chewBBACA, however if you want to install the latest version (>=2.0.16)
Run COREugate
Get COREugate
pip3 install git+https://github.com/kristyhoran/Coreugate
If you are installing COREugate on a server using --user
please ensure that your ~/.local/bin
is part of your PATH
export PATH=$PATH:/path/to/.local/bin
Running COREugate
coreugate [-h] [-v] [--input_file INPUT_FILE]
[--schema_path SCHEMA_PATH]
[--prodigal_training PRODIGAL_TRAINING] [--workdir WORKDIR]
[--threads THREADS]
[--filter_samples_threshold FILTER_SAMPLES_THRESHOLD]
[--cluster] [--cluster_thresholds CLUSTER_THRESHOLDS]
[--force] [--report]
Coreugate - a cgMLST pipeline implementing chewBACCA
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
--input_file INPUT_FILE, -i INPUT_FILE
Input file tab-delimited file3 columns isolate_id
path_to_input_file (contigs) (default: )
--schema_path SCHEMA_PATH, -s SCHEMA_PATH
Path to species schema/allele db (or url if using
chewie Nomenclature server) (default: )
--prodigal_training PRODIGAL_TRAINING, -p PRODIGAL_TRAINING
Prodigal file to be used in allele calling. See https:
//github.com/B-UMMI/chewBBACA/tree/master/CHEWBBACA/pr
odigal_training_files for options (default: )
--workdir WORKDIR, -w WORKDIR
Working directory, default is current directory
(default: /home/khhor/validation/salmonella_typing/rev
erification_20210322)
--threads THREADS, -t THREADS
Number of threads to run chewBACCA (default: 16)
--filter_samples_threshold FILTER_SAMPLES_THRESHOLD, -ft FILTER_SAMPLES_THRESHOLD
The proportion of loci present in a sample for an
sample to be included in further analysis (0-1)
(default: 0.95)
--cluster, -c If you would like to cluster the pairwise distance
matrix. If selected you must provide a list of
thresholds. (default: False)
--cluster_thresholds CLUSTER_THRESHOLDS, -ct CLUSTER_THRESHOLDS
Provide a comma separate list (NO SPACES) eg 20,40,200
(default: )
--force, -f If you want to force chewBBACA to re-run. (default:
False)
--report Save nextflow reports. (default: False)
Display this help message
Sample data
Assemblies
isolate_name path/to/assembly.fa
Species cgMLST schema
COREugate requires an exisiting cgMLST schema, this can be a schema generated by the user or downloaded from one of the publically available databases. These schema should be in the format of a fasta
file for each loci, each file should contain the different alleles for each loci. It should be noted that during allele calling, chewBBACA (implemented by COREugate) will add inferred alleles (more information) to your schema, so it is recommended that the schema path be fixed, that is that the schema is kept in a central location and a single version is used for each species/study.
Other optional arguments
prodigal_training
a prodigal training file for allele calling. Recommended by chewBBACA developers, a list of default training files and further information can be found here.
Limitations of the pipeline
- Coreugate is only able to work with pre-exisiting schemas that have been prep as described above, to derive profiles for isolates.
- Possibly more, I just haven't found them yet!!
Project details
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