Lancet2

Lancet2 is a command line somatic variant caller (SNVs and InDels) for short read sequencing data implemented with modern C++. It performs joint multi-sample localized colored de-bruijn graph assembly for more accurate variant calls, especially InDels.

Installation

Build prerequisites

• Linux x86-64 system
• Git, Make
• GCC (12.x or greater)
• CMake (3.25 or greater)
• BZip2, LibLZMA

Build commands

git clone https://github.com/nygenome/Lancet2.git
cd Lancet2 && mkdir build && cd build
cmake -DCMAKE_BUILD_TYPE=Release .. && make -j$(nproc)

Documentation

Documentation for Lancet2 is hosted on GitHub pages.

Citing

See publications associated with Lancet.

License

Lancet2 is distributed under the BSD 3-Clause License.

Funding

Informatics Technology for Cancer Research (ITCR) under the NCI U01 award 1U01CA253405-01A1.