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‎.github/workflows/deploy.yml

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name: Deploy
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on:
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release:
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types:
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- created
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jobs:
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########################################################################################
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checkout:
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name: Checkout
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strategy:
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matrix:
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machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
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runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: recursive
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########################################################################################
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make:
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name: Make
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needs: checkout
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strategy:
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fail-fast: false
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matrix:
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machine: [x64_linux, arm64_linux, x64_mac, arm64_mac]
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runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']
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steps:
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- name: make
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run: |
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make clean
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make -j32 CXX=g++-12
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- name: tar artifacts
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run: tar -cvzf lz-ani.tar.gz lz-ani LICENSE
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########################################################################################
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help:
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name: Print usage
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needs: make
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strategy:
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fail-fast: false
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matrix:
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machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
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runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']
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steps:
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- name: help
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run: ./lz-ani
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########################################################################################
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upload:
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name: Upload
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needs: help
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strategy:
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fail-fast: false
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matrix:
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machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
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runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']
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steps:
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- name: deploy
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uses: actions/[email protected]
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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with:
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upload_url: ${{ github.event.release.upload_url }}
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asset_path: ./lz-ani.tar.gz
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asset_name: lz-ani-${{ github.event.release.tag_name }}-${{matrix.machine}}.tar.gz
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asset_content_type: application/gzip

‎.github/workflows/main.yml

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name: GitHub Actions CI
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on:
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push:
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branches: [ master, develop, main]
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paths-ignore:
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- '**.md'
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workflow_dispatch:
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jobs:
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########################################################################################
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make:
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name: Make
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strategy:
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fail-fast: false
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matrix:
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machine: [ubuntu-latest, macOS-12]
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runs-on: ['${{ matrix.machine }}']
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: recursive
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- name: make
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run: |
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g++ --version
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make -j CXX=g++-12
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- name: tar artifacts
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run: tar -cvf lz-ani.tar ./lz-ani ./test
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- uses: actions/upload-artifact@v4
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with:
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name: executable-artifact-${{ matrix.machine }}
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path: ./lz-ani.tar
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########################################################################################
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vir61:
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needs: make
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name: Virus data
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strategy:
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fail-fast: false
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matrix:
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machine: [ubuntu-latest, macOS-12]
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runs-on: ['${{ matrix.machine }}']
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steps:
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- uses: actions/download-artifact@v4
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with:
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name: executable-artifact-${{ matrix.machine }}
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path: ./
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- name: untar artifacts
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run: |
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tar -xf lz-ani.tar
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- name: build
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run: |
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./lz-ani all2all --in-dir ./test/vir61 --out ani.tsv
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cmp ani.tsv ./test/vir61.ani.tsv
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‎.github/workflows/self-hosted.yml

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name: Self-hosted CI
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on:
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pull_request:
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branches: [ master, develop, main ]
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paths-ignore:
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- '**.md'
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workflow_dispatch:
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jobs:
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########################################################################################
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checkout:
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name: Checkout
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strategy:
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matrix:
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machine: [tripper, arm64_linux, mac-i7, mac-m1]
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runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: recursive
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########################################################################################
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make:
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name: Make
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needs: checkout
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strategy:
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fail-fast: false
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matrix:
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machine: [tripper, arm64_linux, mac-i7, mac-m1]
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compiler: [12]
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runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']
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steps:
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- name: make (g++-${{matrix.compiler}})
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run: |
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make -j32 CXX=g++-${{matrix.compiler}}
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cp ./lz-ani ./lz-ani-${{matrix.compiler}}
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make clean
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########################################################################################
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help:
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name: Print usage
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needs: make
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strategy:
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fail-fast: false
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matrix:
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machine: [tripper, arm64_linux, mac-i7, mac-m1]
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compiler: [12]
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runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']
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env:
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EXEC: ./lz-ani-${{matrix.compiler}}
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steps:
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- name: help (g++-${{matrix.compiler}})
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run: |
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${EXEC}
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########################################################################################
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vir61:
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name: Vir61
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needs: help
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strategy:
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fail-fast: false
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matrix:
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machine: [tripper, arm64_linux, mac-i7, mac-m1]
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compiler: [12]
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runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']
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env:
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EXEC: ./lz-ani-${{matrix.compiler}}
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steps:
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- name: all2all
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run: |
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${EXEC} all2all --in-dir ./test/vir61 --out ani.tsv
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cmp ani.tsv ./test/vir61.ani.tsv

‎README.md

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# LZ-ANI
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![version](https://img.shields.io/badge/version-1.1.0-blue.svg)
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[![GitHub Actions CI](../../workflows/GitHub%20Actions%20CI/badge.svg)](../../actions/workflows/main.yml)
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[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
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LZ-ANI is a fast and memory-efficient tool for determining average nucleotide identity (ANI) in large sets of genomic sequences. The tool uses Lempel-Ziv parsing, achieving high sensitivity in discerning matched and mismatched nucleotides, thereby enabling accurate determination of ANI. Its efficiency stems from a simplified indel handling model, making LZ-ANI magnitudes faster than alignment-based tools (e.g., BLASTn, MegaBLAST) while maintaining accuracy comparable to the most sensitive BLASTn searches.
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LZ-ANI is a key component of [Vclust](https://github.com/refresh-bio/vclust), a tool for comparing and clustering virus genomes. Although optimized for virus genomes, LZ-ANI's parameters can be customized for longer genomes, such as those of bacteria and archaea.

‎test/vir61.ani.ids.tsv

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id seq_len no_parts
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NC_020483.1 42084 1
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NC_028800.1 41698 1
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NC_023005.1 41386 1
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NC_011043.1 41181 1
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NC_028661.1 41149 1
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NC_013647.1 41119 1
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NC_028977.1 41054 1
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NC_015264.1 40973 1
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NC_015719.1 40940 1
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NC_028822.1 40829 1
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NC_028863.1 40477 1
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NC_024362.1 40472 1
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NC_031943.1 40470 1
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NC_023736.1 40411 1
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NC_021062.1 40192 1
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NC_028688.1 40114 1
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NC_001604.1 39937 1
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NC_022744.1 39860 1
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NC_011040.1 39816 1
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NC_007456.1 39704 1
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NC_031258.1 39696 1
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NC_023548.1 39651 1
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NC_031115.1 39616 1
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NC_001271.1 39600 1
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NC_015208.1 39562 1
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NC_007149.1 39503 1
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NC_011534.1 39472 1
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NC_031123.1 39444 1
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NC_031066.1 39434 1
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NC_019510.1 39282 1
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NC_031018.1 39274 1
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NC_015249.1 39270 1
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NC_011042.1 39252 1
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NC_028655.1 39235 1
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NC_031114.1 39235 1
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NC_023576.1 39207 1
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NC_027292.1 39167 1
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NC_015159.1 39162 1
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NC_031092.1 39158 1
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NC_028772.1 39133 1
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NC_024379.1 39093 1
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NC_031937.1 38979 1
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NC_023558.1 38966 1
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NC_011045.1 38841 1
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NC_010807.1 38815 1
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NC_027387.1 38810 1
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NC_011038.1 38677 1
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NC_025451.1 38646 1
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NC_028880.1 38625 1
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NC_023715.1 38616 1
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NC_008694.1 38564 1
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NC_019416.1 38513 1
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NC_013651.1 38497 1
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NC_011085.3 38457 1
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NC_015271.1 38368 1
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NC_003298.1 38208 1
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NC_028702.1 38084 1
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NC_004777.1 37555 1
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NC_004665.1 37359 1
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NC_029102.1 36051 1
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NC_028795.1 31522 1

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