Kairos assess ===== .. _Kairos assess: see :doc:`installation` for installing .. code-block:: console Description ------------ Kairos assess detects the presence of contigs representing structural microdiversity and/or potential HGTs and reports their presence to the user Input ----------- input to Kairos assess is a contigs fasta file and interleaved fastq files to be mapped **input parameters** * taxa_df = null input taxonomy dataframe of format: contig classification * input_contigs = null input contigs in fasta format * outprefix = 'kairos' job title that will be used for file naming **clustering and window extraction parameters** * edge_length = 75 length in bp to extend around boundaries of alignment (window size is 2*edge_length) * mmseqs_windows_cov = 0.88 the mmseqs -c parameter used during window dereplication * mmseqs_windows_id = 0.99 the mmseqs --id parameter used during window dereplication * mmseqs_windows_cov_mode = 1 the mmseqs -c parameter used during window dereplication **output options**