Burrows-Wheeler Aligner* (BWA*)
A popular software package for mapping low-divergent sequences against a large-reference genome, such as the human genome.
BWA-ALN* 0.5.10
The BWA* project focused on how running the optimized code on an Intel® Xeon® processor and adding an Intel® Xeon Phi™ coprocessor improves modular performance1 and supports symmetric running models on hybrid Intel® Xeon® processors and Intel® Xeon Phi™ coprocessor nodes.
Performance Results
The Intel® Xeon® processor E5-2697 v2 and the Intel® Xeon Phi™ coprocessor symmetric process demonstrated up to 1.86X improved performance over the baseline Intel Xeon processor E5-2697 v2.
Workload is korean_female (read file 3.5 GB, 3.0 GB reference data base).
Related Content
The Removing Load Imbalance in Burrows-Wheeler Sequence Alignment* (BWA-ALN* 0.7.5) white paper focuses on how the use of tools such as Pintools, Intel® VTune™, and Intel® Cilk™ assisted in the optimization of BWA-ALN 0.7.5a. With minimal programming effort, load imbalances were removed and scaling improved, achieving up to a 2X performance improvement.
Genomics Codes
BWA-ALN* 0.5.10
A popular software package for mapping low-divergent sequences against a large-reference genome, such as the human genome.
MPI-HMMER* v2.3
An open-source implementation of the HMMER* protein sequence analysis suite.
BLASTn*/BLASTp*
An algorithm for comparing primary biological sequence information.
GATK*
A software package developed at the Broad Institute to analyze next-generation sequencing data.
QIAGEN
QIAGEN Bioinformatics* solutions deliver faster time to insight by combining powerful analytics that are able to interpret complex biological processes.
Halvade*
Halvade* is a MapReduce implementation of the best-practice DNA sequencing pipeline as recommended by Broad Institute.
ABySS*
ABySS* is an open-source de novo genome assembler for short paired-end reads.
DIDA*
DIDA* performs large-scale alignment tasks by distributing the indexing and alignment stages into smaller subtasks over a cluster of compute nodes.
elPrep*
elPrep* is a high-performance tool for preparing SAM/BAM/CRAM files for variant calling in genomic sequencing pipelines.
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Configuration Table
| System Overview | Intel® Xeon® Processor E5-2697 v2 with Intel® Xeon Phi™ Coprocessor 7120A |
|---|---|
| Platform | Intel® R2208GZ4GC Platform, 2U chassis, hot-swap drives, 24 DIMMs, 1 750W redundant power supply |
| CPU/Stepping | Intel® Xeon® processor E5-2697 v2, 2.7 GHz, 12 core, 8 GT/s dual Intel® QuickPath Interconnect (Intel® QPI) links, 130W, 3.5 GHz max turbo frequency, 768 kB instr L1 / 3072 kB L2 / 30 MB L3 cache |
| Coprocessor | Intel® Xeon® Phi coprocessor 7110 and 7120; 61 cores, 1.1 and 1.238 GHz, error-correcting code (ECC) enabled, Intel® Turbo Boost Technology disabled |
| Software Details | Intel® Manycore Platform Software Stack (Intel® MPSS) version - 2.1.6720-13/16/19, Flash* version - 2.1.03.0386 |
| Memory | Hynix HMT31GR7BFR-PB*, 64 GB total 8*8 GB 1600 MHZ Reg ECC DDR3 |
| Chipset | Rev 4.6, SE5C600.86B.99.99.x069.071520130923 |
| BIOS Configuration | Default except: Intel® Turbo Boost Technology enabled, Enhanced Intel SpeedStep® Technology enabled, surface-mount technology (SMT) enabled, non-uniform memory access (NUMA) enabled, memory speed 1600 MHz, Note: all prefetchers enabled (this is default) |
| GigE Node Adapter | Intel® Ethernet Controller I350 (rev 01), 4 Gigabit network connections, only one connection in use |
| IB Switch | 36-port switch/rack Mellanox FDR* (model MSX6025F-1BFR), Firmware version: 9_2_4002 |
| IB Adapters | 36-port switch/rack Mellanox FDR* (model MSX6025F-1BFR), Firmware version: 9_2_4002 |
| HDD Specs | Seagate ST9600205SS* (scsi), 1x600 GB SAS HDD 10kRPM |
| Operating System | Red Hat Enterprise Linux* 6.4 |
Product and Performance Information
Benchmark results were obtained prior to implementation of recent software patches and firmware updates intended to address exploits referred to as "Spectre" and "Meltdown". Implementation of these updates may make these results inapplicable to your device or system.
Performance varies by use, configuration and other factors. Learn more at www.Intel.com/PerformanceIndex.