Merge multiple Panaroo batch outputs into a single pangenome result

Source: R/data_processing.R

Finds batch output directories under input_path that contain final_graph.gml, and merges them with panaroo-merge inside a Docker container. Output goes to input_path/merge_output.

.mergePanaroo(
  input_path,
  core_threshold = 0.9,
  len_dif_percent = 0.95,
  cluster_threshold = 0.95,
  family_seq_identity = 0.5,
  threads = 8
)

Arguments

input_path

A directory that contains multiple Panaroo pangenome directories for merging.

core_threshold

Numeric. Core genome threshold for Panaroo (--core_threshold). Default 0.90.

len_dif_percent

Numeric. Length difference percentage (--len_dif_percent). Default 0.95.

cluster_threshold

Numeric. Sequence identity threshold (--threshold). Default 0.95.

family_seq_identity

Numeric. Gene family clustering identity (-f). Default 0.5.

threads

Integer. Number of threads for Panaroo and parallel execution. Default 8.

Value

A a single combined pangenome.