From 84b1c201c8f8ca4d0b34e344c70a06a9da20f160 Mon Sep 17 00:00:00 2001 From: Saurabh Date: Tue, 3 Aug 2021 21:45:33 -0700 Subject: [PATCH] Updated README --- README.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 21459d7..7413eda 100644 --- a/README.md +++ b/README.md @@ -5,13 +5,13 @@ mm2-fast is a drop-in replacement of minimap2, providing the same functionality In the current version, all the modules are optimized using **AVX-512** vectorization. ### System requirement -Operating System: Linux -Compiler: G++/ICPC -- version -Architecture: AVX512 -Memory requirement: ~30GB for human genome +Operating System: Linux\\ +Compiler: g++ (GCC) 9.2.0/icpc version 19.1.3.304 \\ +Architecture: AVX512\\ +Memory requirement: ~30GB for human genome\\ ### Installation -clone the fast-contrib branch from minimap2 github page. The source code can be compiled by simple using make command. +Clone the *fast-contrib* branch from minimap2 github page. The source code can be compiled by simple using *make* command. ``` git clone --recursive https://github.com/lh3/minimap2.git -b fast-contrib mm2-fast cd mm2-fast @@ -25,7 +25,7 @@ The usage of mm2-fast is same as minimap2. Here is an example of mapping ONT rea ``` ### Accuracy evaluation -As mm2-fast is an accelerated version of minimap2-v2.18, the output of mm2-fast can be verified against minimap2-v2.18. Note that, AVX512-based chaining in mm2-fast by default runs with a chaining parameter max-skip=infinity for higher chaining precision. Therefore, for correctness verification, minimap2 should run with a larger value of max\_skip parameter. Follow the below steps to verify the accuracy of mm2-fast. +As mm2-fast is an accelerated version of minimap2-v2.18, the output of mm2-fast can be verified against minimap2-v2.18. Note that, AVX512-based chaining in mm2-fast by default runs with a chaining parameter *max-skip=infinity* for higher chaining precision. Therefore, for correctness verification, minimap2 should run with a larger value of *max-skip* parameter. Follow the below steps to verify the accuracy of mm2-fast. ```sh git clone https://github.com/lh3/minimap2.git -b v2.18 cd minimap2 && make @@ -57,7 +57,7 @@ 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. +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