Alignasm is part of the ACCtools pipeline, a project designed to resolve the complex karyotypes of cancer using graph-based approaches. Alignasm takes as input a PAF format file, where a de novo assembled genome has been aligned to a reference. Then, alignasm performs graph-based analysis to infer which references the contigs are likely derived from.
git clone https://github.com/ACCtools/alignasm.git
cd alignasm
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
alignasm <input.paf>
When provided with input.paf as input, it generates two serialized outputs: input.aln.paf, which contains the aligned data, and input.aln.alt.paf, which represents the alternative paths.
It is recommended to have more than 512 GB of RAM available for running alignasm.
For a more detailed pipeline on how to use Alignasm, refer to ACCtools-pipeline.
Kyungmo Ku pentagon03.codes@gmail.com
Hyunwoo Ryu wowo0118@korea.ac.kr