diff --git a/README.md b/README.md index fc02a7d..215f505 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,13 @@ ## mm2-fast ### 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. -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 Operating System: Linux 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 ### Installation @@ -59,7 +59,7 @@ make clean && make lhash=1 use_avx2=1 ### 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. ### 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.