nygenome/Lancet2

v2.x of the microassembly based somatic variant caller

Lancet2

Micro-assembly based somatic variant caller

Note: Lancet2 is currently under development and is not yet ready for production use.

Docker builds

• Docker images are available for every tagged release.
• Please note that the public docker image requires Cascade Lake CPU or newer.
• If needed, users can build an image for any 64-bit Linux machine using the Dockerfile

Installation

Pre-requisites to compile from source

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

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.

Authors

Rajeeva Musunuri, Bryan Zhu and Giuseppe Narzisi

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.