AAA Actino Assembly and Annotation script

The shell script Actino Assembly and Annotation (AAA) was used for assembly, polishing and initial assessment of the strains.

Notice that several outputs from this script was not used for the analysis in the manuscript including:

Gene and functional annotation was done at NCBI using PGAP for a more consistent and reproducible annotation than the Prokka annotation with custom databases in the AAA script.

BUSCO assignment was recreated with the specified databases and versions, the AAA BUSCO assignment was used only for excluding strains with dubious scores (>100 duplicate BUSCOs, <100 identified complete BUSCOs).

Phylogenetic assignment was done using GTDBtk, and the AAA autoMLST assignment was used solely to exclude strains from analysis if the autoMLST assignment suggested culture contamination (e.g. if a bacillus instead of actinomycete was sequenced).

The AAA zip file was downloaded from https://github.com/tuspjo/AAA-Actino-Assembly-and-Annotation/tree/main on 2024-02-02