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Update README.md

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Chirag Jain
2021-08-04 16:01:33 -04:00
committed by Heng Li
parent 38075e82cc
commit a5c14dd5f9
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@@ -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
```