This repository is deprecated

Please use updated tool TREW

TRIS : Telomeric Repeat motif Identification tool with Short-read sequencing

TRIS is tool that can identify Telomeric repeat motif (TRM) with short-read sequencing data. This tool looks for repeated sequences in a single read to find candidates for TRMs, iterating through them to finally find a TRM.

Install

You can download a binary from release or build from source.

Windows (x86_64)
Linux (x86_64)
MacOS (x86_64, arm64)

Install from source

Windows (Visual Studio)

git clone https://github.com/Chemical118/TRIS.git
cd TRIS

git clone https://github.com/Microsoft/vcpkg.git
.\vcpkg\bootstrap-vcpkg.bat

mkdir build
cmake -B build -S . -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=vcpkg\scripts\buildsystems\vcpkg.cmake
cmake --build build --config Release

.\build\Release\tris_test.exe -- test\test.fastq.gz test\test.fastq
.\build\Release\tris.exe -h

Unix

git clone https://github.com/Chemical118/TRIS.git
cd TRIS

git clone https://github.com/Microsoft/vcpkg.git
./vcpkg/bootstrap-vcpkg.sh

mkdir build
cmake -B build -S . -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=vcpkg/scripts/buildsystems/vcpkg.cmake
cmake --build build

./build/tris_test.exe -- test/test.fastq.gz test/test.fastq
./build/tris -h

Quick Start

tris MIN_MER MAX_MER <short_read_data1.fastq.gz> <short_read_data2.fastq>... -t <number of threads> 

MIN_MER : minimum length of sequence to find telomere [MIN_MER >= 3]
MAX_MER : maximum length of sequence to find telomere [MAX_MER <= 64]

The following is a recommended command line to run TRIS.

tris 5 32 <short_read_data1.fastq.gz> <short_read_data2.fastq>... -t <number of threads> 

Output

><short_read_data1.fastq.gz>
<length of repeat>,<repeat sequence>,<number of repeat>
...

><short_read_data2.fastq.gz>
<length of repeat>,<repeat sequence>,<number of repeat>
...

Author

Hyunwoo Ryu wowo0118@korea.ac.kr

Special thanks to
Jiho Choi sdatoli@korea.ac.kr
Kyungmo Ku kyungmoku7141@gmail.com