FastGT 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. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the frequency of k-mers in sequencing data and predicts the genotype. All this takes less than 1 hour on average low-cost Linux server.

    You need to download the following components:

  • At least one database file with k-mers from this webpage
  • Two main binaries of FastGT: gmer_counter and gmer_caller
  • FASTQ file with Illumina reads

The manuscript is available from biorXiv, official peer-reviewed version is available from

If you use FastGT software, please cite Pajuste et al. Scientific Reports 7: 2537 (2017).

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