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Chirag Jain
2021-08-04 16:01:33 -04:00
committed by Heng Li
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## mm2-fast ## mm2-fast
### Introduction ### Introduction
mm2-fast is an accelerated implementation of minimap2 on modern CPUs. mm2-fast accelerates all three major modules of minimap2: Seeding, Chaining, and Alignment, achieving up to 3.5x speedup over minimap2. mm2-fast is an accelerated implementation of minimap2 on modern CPUs. mm2-fast accelerates all the three major modules of minimap2: (a) seeding, (b) chaining, and (c) pairwise alignment, achieving up to 3.5x speedup over minimap2.
mm2-fast is a drop-in replacement of minimap2, providing the same functionality with the exact same output. mm2-fast is a drop-in replacement of minimap2, providing the same functionality with the exact same output.
In the current version, all the modules are optimized using **AVX-512** vectorization. In the current version, all the modules are optimized using **AVX-512** vectorization. Detailed benchmark results are available in our [preprint](https://doi.org/10.1101/2021.07.21.453294).
### System requirement ### System requirement
Operating System: Linux Operating System: Linux
Compiler: g++ (GCC) 9.2.0/icpc version 19.1.3.304 Compiler: g++ (GCC) 9.2.0/icpc version 19.1.3.304
Architecture: AVX512 Architecture: [AVX512](https://en.wikipedia.org/wiki/AVX-512)
Memory requirement: ~30GB for human genome Memory requirement: ~30GB for human genome
### Installation ### Installation
@@ -59,7 +59,7 @@ make clean && make lhash=1 use_avx2=1
### Future Plans ### Future Plans
The current version of mm2-fast is based on minimap2-v2.18. We are planning to apply our optimizations to minimap2 master branch. The current version of mm2-fast is based on minimap2-v2.18. We are planning to apply our optimizations to minimap2 master branch.
### Citations ### Citations
"Accelerating long-read analysis on modern CPs"; Saurabh Kalikar, Chirag Jain, Vasimuddin Md, Sanchit Misra; uploaded to bioRxiv - https://www.biorxiv.org/content/10.1101/2021.07.21.453294v1 ["Accelerating long-read analysis on modern CPUs"](https://doi.org/10.1101/2021.07.21.453294); Saurabh Kalikar, Chirag Jain, Vasimuddin Md, Sanchit Misra; BioRxiv 2021
The original README content of minimap2 follows. The original README content of minimap2 follows.