Core genome determination¶
Core genomes can be calculated by three different means. Core genomes definition from ridom and enterobase are already included in the Docker image, in the folder /home/pipeline_user/core_genomes/cgMLST, and the references they use in /home/pipeline_user/references/.
Ridom¶
cgMLST scheme from ridom can be extracted directly for theses species
| Species | Taxonomy ID | Ridom ID | Reference genome assembly ID |
|---|---|---|---|
| Acinetobacter_baumannii | 470 | 3956907 | 39528 |
| Enterococcus_faecium | 1352 | 991893 | 526908 |
| Klebsiella_pneumoniae | 573 | 2187931 | 31388 |
| Listeria_monocytogenes | 1639 | 690488 | 264498 |
| Legionella_pneumophila | 446 | 1025099 | 30068 |
| Mycobacterium_tuberculosis | 1773 | 741110 | 538048 |
| Staphylococcus_aureus | 1280 | 141106 | 33148 |
| Clostridioides_difficile | 1496 | 3560802 | 6374038 |
A bed file is constructed from the locus target file, using coordinates from the start and length columns of the csv file file available on the ridom website.
Example¶
snakemake --snakefile $pipeline_folder/workflows/core_genome/make_ridom.rules \
core_genomes/cgMLST/Staphylococcus_aureus.bed \
--use-conda --conda-prefix $conda_folder
will create a BED file in core_genomes/cgMLST/Staphylococcus_aureus.bed which defines the core genomic regions in the genome of the assembly ID 33148 (Staphylococcus aureus COL).
Enterobase¶
cgMLST scheme from enterobase is available for:
| Species | Taxonomy ID | Enterobase ID | Reference genome assembly ID | Scheme |
|---|---|---|---|---|
| Escherichia_coli | 562 | ESCwgMLST | 79781 | cgMLSTv1 |
| Salmonella_enterica | 28901 | SALwgMLST | 359488 | cgMLSTv1 |
A bed file for each reference genome, based on the locus tags present in this genome, is constructed. For instance, over the 3002 loci of the Salmonella cgMLSTv1, 69 come from a different genome than the reference 359488. For E. coli, only 15 loci are missing for the reference assembly (79781), out of 2498.
Example¶
snakemake --snakefile $pipeline_folder/workflows/core_genome/make_enterobase.rules \
core_genomes/cgMLST/Salmonella_enterica.bed \
--use-conda --conda-prefix $conda_folder
will create a BED file in core_genomes/cgMLST/Salmonella_enterica.bed defining the core genomic regions in the genome of the assembly ID 359488 (Salmonella enterica subsp. enterica serovar Typhimurium str. D23580).
ParSNP¶
For species unavailable on either resource, core genome can be calculated using parsnp and the complete genomes of the species available on RefSeq. As ParSNP is not available on bioconda, the binary must be downloaded from the ParSNP website and placed in your $PATH.
Example¶
snakemake --snakefile $pipeline_folder/workflows/core_genomes/make_parsnp.rules \
core_genome/parsnp/Morganella_morganii/parsnp.xmfa \
--use-conda --conda-prefix $conda_folder
will calculate the core genome with parSNP with every complete genome of Morganella morganii available in RefSeq.
If you wish to create a new parSNP core genome definition with the Docker image (that include the parsnp binary), do not link any references or core_genomes from your working directory.