HAlign-G

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A rapid and low-memory multiple-genome aligner for closely related genomes

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# HAlign-G: A rapid and low-memory multiple-genome aligner for large-scale closely related genomes
HAlign-G is a tool written in C++ for aligning multiple gemones. It runs on Linux and Windows.

## Installation
### Linux/WSL (Windows Subsystem for Linux) - from Anaconda
1.Install WSL for Windows. Instructional video [1](https://www.youtube.com/watch?v=X-DHaQLrBi8&t=5s) or [2](http://lab.malab.cn/%7Etfr/1.mp4) (Copyright belongs to the original work).

2.Download and install Anaconda. Download Anaconda for different systems [here](https://www.anaconda.com/products/distribution#Downloads). Instructional video of anaconda installation [1](https://www.youtube.com/watch?v=AshsPB3KT-E) or [2](http://lab.malab.cn/%7Etfr/Install_anaconda_in_Linux.mp4) (Copyright belongs to the original work).

3.Install HAlign-G.
```bash
#1 Create and activate a conda environment for HAlign-G
conda create -n haligng_env
conda activate haligng_env

#2 Add channels to conda
conda config --add channels malab
conda config --add channels conda-forge

#3 Install HAlign-G
conda install -c malab -c conda-forge halign-g

#4 Test HAlign-G
halign-g -h
```

## Usage
```
Usage of halign-g2:
halign-g Input_file Output_file [-r/--reference val] [-p/--threads val] [-bwt/--bwt val] [-dc/--divide_conquer val] [-sv/--svLen val] [-h/--help]
        Input_file      :  Input file/folder path[Please use .fasta as the file suffix or a forder]
        Output_file     :  Output file path[Please use .maf or .fasta as the file suffix]
        -r/--reference            : The reference sequence name [Please delete all whitespace] (defualt value:[Longest])
        -p/--threads              : The number of threads (defualt value:1)
        -bwt/--bwt                : The global BWT threshold (defualt value:15)
        -dc/--divide_conquer      : The divide & conquer Kband threshold (defualt value:10000)
        -sv/--svLen               : The structure variation length threshold (defualt value:200)
        -h/--help                 : Show this help message (defualt value:false)
```
HAlign-G1 is designed for multiple sequence alignment (MSA). Among the three versions, it provides the highest alignment quality and supports both FASTA and MAF formats.
```
Usage of halign-g2:
halign-g2 Input_file Output_file [-r/--reference val] [-p/--threads val] [-dc/--divide_conquer val] [-h/--help]
        Input_file      :  Input file/folder path[Please use .fasta as the file suffix or a forder]
        Output_file     :  Output file path[Please use .maf or .fasta as the file suffix]
        -r/--reference            : The reference sequence name [Please delete all whitespace] (defualt value:[Longest])
        -p/--threads              : The number of threads (defualt value:1)
        -dc/--divide_conquer      : The divide & conquer Kband threshold (defualt value:10000)
        -h/--help                 : Show this help message (defualt value:false)
```
HAlign-G2 is tailored for multi-genome alignment within the same species. It is optimized to detect a greater number of structural variations, while also supporting both FASTA and MAF formats.
```
Usage of halign-mum:
halign-mum Input_file Output_file [-r/--reference val] [-t/--threads val] [-l/--load val] [-f/--filter val] [-m/--memory val] [-h/--help]
        Input_file      :  Input folder path
        Output_file     :  Output file path[Please use .maf or .hal as the file suffix]
        -r/--reference            : The reference file name (defualt value:[Longest])
        -t/--threads              : The number of threads (defualt value:32)
        -l/--load                 : Whether the second run and the result directory has a postfix structure file (defualt value:0)
        -f/--filter               : Filter-level: 0-None, 1-General, 2-Strict (defualt value:2)
        -m/--memory               : Maximum available memory / GB (defualt value:28)
        -h/--help                 : Show this help message (defualt value:false)
```
HAlign-MUM is part of the HAlign-G2 framework, built on the same algorithmic logic, but extended to support cross-species genome alignment. Unlike HAlign-G1 and G2, it only supports the MAF format.
## Contacts
The software tools are developed and maintained by [ZOU's lab](http://lab.malab.cn/~zq/en/index.html).

More tools and infomation can visit our [github](https://github.com/malabz).

HAlign-G

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