Kairos assess

see Installation for installing

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

<work in progress>