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Updated README

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Saurabh
2021-08-04 16:01:33 -04:00
committed by Heng Li
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README.md
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@@ -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. In the current version, all the modules are optimized using **AVX-512** vectorization.
### System requirement ### System requirement
Operating System: Linux Operating System: Linux\\
Compiler: G++/ICPC -- version Compiler: g++ (GCC) 9.2.0/icpc version 19.1.3.304 \\
Architecture: AVX512 Architecture: AVX512\\
Memory requirement: ~30GB for human genome Memory requirement: ~30GB for human genome\\
### Installation ### 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 git clone --recursive https://github.com/lh3/minimap2.git -b fast-contrib mm2-fast
cd 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 ### 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 ```sh
git clone https://github.com/lh3/minimap2.git -b v2.18 git clone https://github.com/lh3/minimap2.git -b v2.18
cd minimap2 && make cd minimap2 && make
@@ -57,7 +57,7 @@ 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 CPs"; Saurabh Kalikar, Chirag Jain, Vasimuddin Md, Sanchit Misra; uploaded to bioRxiv - https://www.biorxiv.org/content/10.1101/2021.07.21.453294v1