tandem

tandem is a small C++14 library for finding tandem repeats in strings. At the moment it only finds exact repeats, but I may extend this at some point to find approximate repeats.

main.cpp includes a simple command line tool for DNA/RNA sequences. You can build it with CMake:

$ mkdir build && cd build
$ cmake ..
$ make

The command line tool reads an input stream and reports repeats:

echo NNNACGTACGTNNAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGNNNNNNNN | ./tandem

To find repeats in a FASTA reference genome, you can use the command line tool found in my project bioio:

./fasta human_g1k_v37.fasta Y | ./tandem

To report all repeats in CSV format, add -c -a to the command:

./fasta human_g1k_v37.fasta Y | ./tandem -c -a