Subclustering with PopPIPE



PopPIPE is still a work-in-progress and may not immediately work on your data. We anticipate finalising the pipeline in the near future.


You can run PopPIPE on your PopPUNK output, which will run subclustering and visualisation within your strains. The pipeline consists of the following steps:

  • Split files into their strains.
  • Calculate core and accessory distances within each strain.
  • Use the core distances to make a neighbour-joining tree.
  • (lineage_clust mode) Generate clusters from core distances with lineage clustering in PopPUNK.
  • Use ska to generate within-strain alignments.
  • Use IQ-TREE to generate an ML phylogeny for each strain using this alignment, and the NJ tree as a starting point.
  • Use fastbaps to generate subclusters which are partitions of the phylogeny.
  • Create an overall visualisation with both core and accessory distances, as in PopPUNK. The final tree consists of refining the NJ tree by grafting the maximum likelihood trees for subclusters to their matching nodes.

An example DAG for the steps (excluding ska index, for which there is one per sample):

Example DAG for a PopPIPE run


PopPIPE is a snakemake pipeline, which depends upon snakemake and pandas:

conda install snakemake pandas

Other dependencies will be automatically installed by conda the first time you run the pipeline. You can also install them yourself and omit the -use-conda directive to snakemake:

conda create -n poppipe --file=environment.yml

Then clone the repository:

git clone


  1. Modify config.yml as appropriate.
  2. Run snakemake --cores <n_cores> --use-conda.

On a cluster or the cloud, you can use snakemake’s built-in --cluster argument:

snakemake --cluster qsub -j 16 --use-conda

See the snakemake docs for more information on your cluster/cloud provider.

Alternative runs

For quick and dirty clustering and phylogenies using core distances from pp-sketchlib alone, run:

snakemake --cores <n_cores> --use-conda lineage_clust

To create a visualisation on microreact:

snakemake –use-conda make_microreact

Config file

PopPIPE configuration

  • script_location: The scripts/ directory, if not running from the root of this repository
  • poppunk_db: The PopPUNK HDF5 database file, without the .h5 suffix.
  • poppunk_clusters: The PopPUNK cluster CSV file, usually poppunk_db/poppunk_db_clusters.csv.
  • poppunk_rfile: The --rfile used with PopPUNK, which lists sample names and files, one per line, tab separated.
  • min_cluster_size: The minimum size of a cluster to run the analysis on (recommended at least 6).

IQ-TREE configuration

  • enabled: Set to false to turn off ML tree generation, and use the NJ tree throughout.
  • mode: Set to full to run with the specified model, set to fast to run using --fast (like fasttree).
  • model: A string for the -m parameter describing the model. Adding +ASC is recommended.

fastbaps configuration

  • levels: Number of levels of recursive subclustering.
  • script: Location of the run_fastbaps script. Find by running system.file("run_fastbaps", package = "fastbaps") in R.

Updating a run

Running snakemake from the same directory will keep outputs where possible, so new additions will automatically be included.

TODO: How to do this when adding new isolates with poppunk_assign