KATK is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. KATK uses a list of region-specific k-mers that are unique in human genome, retrieves the reads from corresponding region, aligns these reads and calls variant genotypes from each region. The entire process takes less than 2 hours on average low-cost Linux server.

    To start calling you will need the following components:

  • Two main binaries of KATK: gmer_counter and gassembler from this webpage or from Github
  • A binary file with region-specific k-mers from this webpage
  • A text file with region coordinates from this webpage
  • FASTQ file with Illumina reads

If you have any questions, suggestions or problems with the program, please let us know.