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.

In addition to variant calling accuracy and improved somatic filtering, Lancet2 has significant runtime performance improvements compared to Lancet1 (upto ∼10x speedup and 50% less peak memory usage)

Installation

Pixi / Bioconda (Recommended)

Lancet2 is natively distributed and dynamically linked via the global Bioconda network, with full native Cloud I/O support (s3://, gs://, http(s)://, etc.) completely enabled cleanly by default out of the box.

For significantly faster and strictly isolated local environment resolution, the recommended method is using Pixi:

pixi global install lancet2

Alternatively, using the standard Conda ecosystem:

conda install -c bioconda lancet2

Build prerequisites

• Linux or macOS (x86-64 or ARM64 architectures)
• Git, Make
• GCC (12.x or greater) or Clang (14.x or greater)
• CMake (3.25 or greater)
• BZip2, LibLZMA
• CURL and OpenSSL (optional, required for native Cloud I/O)

Build commands

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

cmake -DCMAKE_BUILD_TYPE=Release -DLANCET_BUILD_STATIC=OFF -DLANCET_ENABLE_CLOUD_IO=ON ..
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.