A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.
The system has been tested on all the AWS G3 and P3 GPU instances with AMI Ubuntu Server 18.04 LTS (HVM), SSD Volume Type (ami-0fc20dd1da406780b (64-bit x86))
- Clone SegAlign repository (https://github.com/gsneha26/SegAlign)
$ git clone https://github.com/gsneha26/SegAlign.git
$ export PROJECT_DIR=$PWD/SegAlign
The following dependencies are required by SegAlign:
- NVIDIA CUDA 10.2 toolkit
- CMake 3.8
- Intel TBB library
- libboost-all-dev
- parallel
- zlib
- LASTZ 1.04.03
- faToTwoBit, twoBitToFa (from kentUtils)
The dependencies can be installed with the given script as follows, which might take a while (only installs the dependencies not present already). This script requires sudo to install most packages at the system level. Using the -c option skips CUDA installation.
$ cd $PROJECT_DIR
$ ./scripts/installUbuntu.sh
- Run SegAlign
$ run_segalign target query [options]
- For a list of options
$ run_segalign --help
$ cd $PROJECT_DIR
$ mkdir test
$ cd test
$ wget https://hgdownload.soe.ucsc.edu/goldenPath/ce11/bigZips/ce11.2bit
$ wget https://hgdownload-test.gi.ucsc.edu/goldenPath/cb4/bigZips/cb4.2bit
$ twoBitToFa ce11.2bit ce11.fa
$ twoBitToFa cb4.2bit cb4.fa
$ run_segalign ce11.fa cb4.fa --output=ce11.cb4.maf
- Run SegAlign repeat masker
$ run_segalign_repeat_masker sequence [options]
- For a list of options
$ run_segalign_repeat_masker --help
$ cd $PROJECT_DIR
$ mkdir test_rm
$ cd test_rm
$ wget https://hgdownload.soe.ucsc.edu/goldenPath/ce11/bigZips/ce11.2bit
$ twoBitToFa ce11.2bit ce11.fa
$ run_segalign_repeat_masker ce11.fa --output=ce11.seg
S. Goenka, Y. Turakhia, B. Paten and M. Horowitz, "SegAlign: A Scalable GPU-Based Whole Genome Aligner," in 2020 SC20: International Conference for High Performance Computing, Networking, Storage and Analysis (SC), Atlanta, GA, US, 2020 pp. 540-552. doi: 10.1109/SC41405.2020.00043