Table 1 Pipelines used for the cluster congruence analysis with indication of the input type, the schema or reference genome used for each species, the output used for clustering and the clustering method(s) applied
Pipeline name | Workflow | Type of pipeline | Input type | Schema (if allele) / Type of dataset (if SNP) | Output for clustering | Clustering method | |||
|---|---|---|---|---|---|---|---|---|---|
L. monocytogenes | S. enterica | E. coli | C. jejuni | ||||||
chewieSnake | chewieSnake | Allele | Assembly | Ruppitsch | Enterobase | Enterobase | PubMLST | Allele matrix | HC and GT |
INNUENDO-like (Listeria) or INNUENDO-like-schema | INNUENDO-like* | Allele | Assembly | Moura | INNUENDO wgMLST/INNUENDO cgMLST§ (EFSA)/Enterobase | INNUENDO wgMLST/INNUENDO cgMLST§ (EFSA)/Enterobase | INNUENDO wgMLST/INNUENDO cgMLST/PubMLST | Allele matrix | HC and GT |
SeqSphere or SeqSphere-wgMLST (C. jejuni) | Ridom SeqSphere + ** | Allele | Assembly | Ruppitsch | Enterobase | Enterobase | SeqSphere (extended) | Allele or Distance or Partition table | HC and GT |
Bionumerics | Bionumerics** | Allele | Assembly | Moura | Enterobase | Enterobase | Oxford | Distance matrix | HC |
MentaLiST | MentaLiST | Allele | Assembly | Moura | INNUENDO | INNUENDO | INNUENDO | Allele matrix | HC and GT |
SnippySnake | SnippySnake | SNP | Reads | ST | serotype | serotype | - | Distance matrix | HC |
CSI | CSI Phylogeny | SNP | Reads | ST*** | serotype*** | serotype | ST | Distance matrix | HC |
WGSBAC | WGSBAC | SNP | Reads | ST | serotype | serotype | - | Distance matrix | HC |
SnapperDB | SnapperDB | SNP | Reads | - | serotype | - | - | Distance matrix | HC |
