Manual

Annotate

  1. annotate: Annotate genomic assemblies with bakta.

Cluster

  1. extract: Extract sequences and annotations from GFF files.
  2. collect: Collect extracted sequences from multiple samples into one file.
  3. cluster: Cluster nucleotide sequences with mmseqs.
  4. defrag: Defrag clusters by associating fragments with their parent cluster.
  5. summarize: Summarize clusters according to their annotations.

Align

  1. align: Align clusters using mafft and create a pangenome alignment.

Variants

  1. structural: Extract structural variants from cluster alignments.
  2. snps: Extract SNPs from a pangenome alignment.
  3. presence_absence: Extract presence absence of clusters.

Tree

  1. tree: Estimate a maximum-likelihood tree with IQ-TREE.

GWAS

  1. gwas: Run genome-wide association study (GWAS) tests with pyseer.

Plot

  1. manhattan: Plot the distribution of variant p-values across the genome.
  2. heatmap: Plot a heatmap of variants alongside a tree.

Utility

  1. root_tree: Root tree on outgroup taxa.
  2. binarize: Convert a categorical column to multiple binary (0/1) columns.
  3. table_to_rtab: Convert a TSV/CSV table to an Rtab file based on regex filters.
  4. vcf_to_rtab: Convert a VCF file to an Rtab file.

Overview