diff --git a/README.md b/README.md index ace1064..dfdd2c4 100644 --- a/README.md +++ b/README.md @@ -38,14 +38,12 @@ diff minimap2_output mm2-fast_output > diff_result The file diff\_result should show a clean-diff with the difference of 2 lines, i.e., the lines containing the command-line parameters for minimap2 and mm2-fast. ### Advanced options -The default compilation using make applies two optimizations: AVX512 vectorized chaining and alignment, and learned-indexes based seeding is disabled by default as it requires aditional installations. Learned hash-table uses an external training library that runs on [Rust](https://en.wikipedia.org/wiki/Rust_(programming_language)). Following are the steps to enable learned hash table optimization in mm2-fast: +The default compilation using make applies two optimizations: AVX512 vectorized chaining and alignment, and learned-indexes based seeding is disabled by default as it requires availability of [Rust](https://en.wikipedia.org/wiki/Rust_(programming_language)). This is because the learned hash-table uses an external training library that runs on Rust. Rust is trivial to install, see https://rustup.rs/ and add its path to .bashrc file. Following are the steps to enable learned hash table optimization in mm2-fast: ```sh -# Compile and run mm2-fast with optimized seeding -1. Build learned hash table index for optimized seeding module - Pre-requisite: Install "Rust" and add path to .bashrc file. Rust is trivial to install, see https://rustup.rs/ - ./build_rmi.sh test/MT-human.fa map-ont ##takes two arguments: 1. path-to-reference-seq-file 2. preset +# Start by building learned hash table index for optimized seeding module +./build_rmi.sh test/MT-human.fa map-ont ##takes two arguments: 1. path-to-reference-seq-file 2. preset -2. Compile and run +# Next, compile and run the mapping phase make clean && make lhash=1 ./minimap2 -ax map-ont test/MT-human.fa test/MT-orang.fa > mm2-fast-lhash_output ```