GenomeTester4

A toolkit for performing set operations - union, intersection and complement - on k-mer lists.
Copyright (C) University of Tartu 2015-2016.
Please cite: Kaplinski L, Lepamets M, Remm M. (2015). GenomeTester4: a toolkit for performing basic set operations – union, intersection and complement on k-mer lists. GigaScience, 4:58

Building GenomeTester4 binaries:
Change into subdirectory 'src' and type:

make clean
make

FastGT

An alignment-free genotype caller.
Copyright (C) University of Tartu 2015-2017
Please cite: Pajuste F-D, Kalpinski L, Möls M, Puurand T, Lepamets M, Remm M. (2017). FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads. Scientific Reports, 7:2537

FastGT is implemented as a sub-project of GenomeTester4, sharing some source files.
Source files are inside the GenomeTester4 distribution.
FastGT utilizes two binaries from the GenomeTester4 package: gmer_counter and gmer_caller.

Building FastGT binaries:

git clone https://github.com/bioinfo-ut/GenomeTester4.git
cd GenomeTester4/
cd src
make gmer_counter
make gmer_caller

• k-mer lists and user manual for FastGT are available from http://bioinfo.ut.ee/FastGT/ See also README.FastGT.md

KATK

A genotype caller for rare and de novo variants.
Copyright (C) University of Tartu 2016-2021

KATK is implemented as a sub-project of GenomeTester4, sharing some source files.
Source files are inside the GenomeTester4 distribution.
KATK utilizes two binaries from the GenomeTester4 package: gmer_counter and gassembler.

Building KATK binaries:

git clone https://github.com/bioinfo-ut/GenomeTester4.git
cd GenomeTester4/
cd src
make gmer_counter
make gassembler

• KATK data files required for calling variants from the entire exome are available from http://bioinfo.ut.ee/KATK/ See also README.KATK.md