gsneha26 / Darwin-WGA

Co-processor for whole genome alignment

Darwin-WGA

A co-processor for whole genome alignment.

Table of Contents

• Getting Started
• Design Overview
• Building and Running tests
  • Steps for hardware emulation (MODE-hw_emu)
  • Steps for running on the EC2 F1 instance, f1.2xlarge (MODE-hw)
• Citing Darwin-WGA

Getting Started

The system has been tested on AWS EC2 F1 instance, f1.2xlarge with AMI 1.4.0 (https://amzn.to/2zfsjCM and click on Continue to Subscribe).

• Install dependencies

    $ sudo yum install cmake
    $ sudo yum install zlib-devel zlib-static

• Clone aws-fpga directory (https://github.com/aws/aws-fpga)

    $ git clone https://github.com/aws/aws-fpga.git
    $ export AWS_DIR=$PWD/aws-fpga
    $ source $AWS_DIR/sdaccel_setup.sh

• Clone Darwin-WGA repository (https://github.com/gsneha26/Darwin-WGA)

    $ git clone https://github.com/gsneha26/Darwin-WGA.git
    $ export PROJECT_DIR=$PWD/Darwin-WGA

• Clone tbb package (https://github.com/01org/tbb)

    $ cd $PROJECT_DIR
    $ git clone https://github.com/01org/tbb 

• Copy kseq.h from https://github.com/lh3/ksw2

    $ cd $PROJECT_DIR
    $ wget https://github.com/lh3/ksw2/blob/master/kseq.h
    $ mv kseq.h $PROJECT_DIR/src/host/WGA/

Design Overview

As described in the paper, Darwin-WGA is based on the seed-filter-extend paradigm.

As shown above, the implementation is divided between software and hardware (FPGA/ASIC). Seeding is done using D-SOFT algorithm in software. Filtering uses Banded Smith-Waterman (BSW) modules in FPGA. Extension used GACT-X modules in FPGA. BSW and GACT-X modules consist of individual tests

The project consists of tests for individual BSW and GACT-X modules. The complete system is also tested under the module name WGA.

Building and Running tests

The process is described in detail in aws-fpga/SDAccel/README.md. The steps specific to this project are described below.

• Package the hdl files into XO files. A new folder, xclbin/ consists of all the .xo files required in the project.

    $ cd $PROJECT_DIR 
    $ ./scripts/create_xo.sh 

Steps for hardware emulation (MODE-hw_emu)

  $ cd $PROJECT_DIR 
  $ ./scripts/create_{BSW/GACTX/WGA}.hw_emu.sh
  $ cd test_{BSW/GACTX/WGA}_hw_emu
  $ export LD_LIBRARY_PATH=$XILINX_SDX/runtime/lib/x86_64/:$LD_LIBRARY_PATH
  $ export XCL_EMULATION_MODE=hw_emu

Parameters for each module are specified in params.cfg.

Banded Smith-Waterman (BSW)

ref.txt and query.txt consist of the reference and query sequences. Each line in parameters.txt consist of a request specified as {request reference length, request query length, reference start address, query start address}

  $ ./bsw BSW.hw_emu.xclbin {number of tiles as specified in parameters.txt}

In the current example,

  $ ./bsw BSW.hw_emu.xclbin 4

GACT-X

ref.txt and query.txt consist of the reference and query sequences. Each line in parameters.txt consist of a request specified as {request reference length, request query length, reference start address, query start address}

  $ ./gactx GACTX.hw_emu.xclbin

Darwin-WGA

Reference and Query sequences should be in the FASTA format and the path should be replaced in params.cfg. For the current example, the sequences are $PROJECT_DIR/data/ce11.fa and $PROJECT_DIR/data/cb4.fa.

  $ ./wga WGA.hw_emu.xclbin

Steps for running on the EC2 F1 instance, f1.2xlarge (MODE-hw)

  $ cd $PROJECT_DIR 
  $ ./scripts/create_{BSW/GACTX/WGA}.hw.sh
  $ cd test_{BSW/GACTX/WGA}_hw
  $ $SDACCEL_DIR/tools/create_sdaccel_afi.sh -xclbin={BSW/GACTX/WGA}.hw.xclbin \ 
    -o=<{BSW/GACTX/WGA}.hw> -s3_bucket=<bucket-name> \
    -s3_dcp_key=<dcp-folder-name> -s3_logs_key=<logs-folder-name>
  $ export LD_LIBRARY_PATH=$XILINX_SDX/runtime/lib/x86_64/:$LD_LIBRARY_PATH
  $ export XCL_EMULATION_MODE=hw
  $ sudo sh
    # source $AWS_DIR/sdaccel_runtime_setup.sh

Banded Smith-Waterman (BSW)

ref.txt and query.txt consist of the reference and query sequences. Each line in parameters.txt consist of a request specified as {request reference length, request query length, reference start address, query start address}

  $ ./bsw BSW.hw_emu.xclbin {number of tiles as specified in parameters.txt}

In the current example,

    # ./bsw BSW.hw.awsxclbin 4

GACT-X

ref.txt and query.txt consist of the reference and query sequences. Each line in parameters.txt consist of a request specified as {request reference length, request query length, reference start address, query start address}

    # ./gactx GACTX.hw.awsxclbin

Darwin-WGA

Reference and Query sequences should be in the FASTA format and the path should be replaced in params.cfg. For the current example, the sequences are $PROJECT_DIR/data/ce11.fa and $PROJECT_DIR/data/cb4.fa.

    # ./wga WGA.hw.awsxclbin

Citing Darwin-WGA

• Seed-filter-extend algorithms and hardware for BSW and GACT-X described in:

  • Turakhia, Y., Goenka, S. D., Bejerano, G., & Dally, W. J. (2019, February). Darwin-WGA: A co-processor provides increased sensitivity in whole genome alignments with high speedup. In 2019 IEEE International Symposium on High Performance Computer Architecture (HPCA) (pp. 359-372). IEEE.

• D-SOFT algorithm and hardware for GACT described in:

  • Turakhia, Y., Bejerano, G., & Dally, W. J. (2018, March). Darwin: A genomics co-processor provides up to 15,000 x acceleration on long read assembly. In ACM SIGPLAN Notices (Vol. 53, No. 2, pp. 199-213). ACM.