RaMA (Rare Match Aligner) is a high-performance tool specialized in pairwise centromere alignment, optimized for ultra-long tandem repeats in complex genomic regions. Leveraging rare matches as anchors and a 2-piece affine gap cost model, RaMA is specifically designed for aligned centromere sequences, delivering highly accurate and efficient pairwise alignments for assembled centromere regions.
RaMA can be installed using two methods: via conda or by compiling the source code.
- If you want to quickly get started with RaMA, we highly recommend using the conda installation method.
- if you prefer to customize RaMA, such as enabling M64 mode to handle ultra-large-scale data (not generally recommended) or using different instruction sets to accelerate alignment, we suggest installing from the source code.
We highly recommand you install RaMA via conda. Simply run the following command:
conda create -n RaMA
conda activate RaMA
conda install -c malab -c conda-forge rama
RaMA -h
Before installing RaMA, ensure your Linux system meets the following requirements:
- GCC version 9 or higher. (Required)
- CMake version 3.1 or higher. (Required)
Start by cloning the RaMA repository along with its submodules. Ensure that Alignment/WFA2-lib is downloaded properly:
git clone --recursive https://github.com/metaphysicser/RaMA.gitNavigate to the RaMA directory, create a build directory, and compile the program:
cd RaMA
mkdir build && cd build
cmake .. -DCMAKE_BUILD_TYPE=Release
make -j$(nproc)
./RaMA -hCompilation Flags Customize your build with additional flags if necessary:
# Enable 64-bit mode
cmake .. -DCMAKE_BUILD_TYPE=Release -DUSE_M64=ON
# Use extra compiler flags, e.g., for AVX2 support
cmake .. -DCMAKE_BUILD_TYPE=Release -DEXTRA_FLAGS="-mavx2"Execute RaMA by specifying the input FASTA file and the output directory:
RaMA -r /path/to/ref.fasta -q /path/to/query.fasta -o /path/to/output_dirNote! Both ref.fasta and query.fasta should contain only one sequence.
Control RaMA's behavior with the following arguments:
Arguments:
-h, --help Show this help message and exit
-r, --reference Reference FASTA file path containing the reference sequences for alignment.
-q, --query Query FASTA file path containing the query sequences for alignment.
-o, --output Output directory path for saving alignment results and additional files.
-t, --threads Number of threads for the alignment process. Defaults to the number of available cores if unspecified.
-s, --save Saves anchor binary files to the output directory for future use, including SA, LCP, and Linear Sparse Table.
-l, --load Loads existing anchor binary files from the output directory to skip SA, LCP, and Linear Sparse Table construction.
-c, --max_match_count Maximum number of rare matches to use for anchor finding. Altering this value is generally not recommended.
-m, --match Match score for sequence alignment. Lower values favor matching characters. Default is 0.
-x, --mismatch Mismatch penalty. Higher values penalize mismatches more. Default is 3.
-g, --gap_open1 Penalty for initiating a short gap. Key for handling different gap lengths. Default is 4.
-e, --gap_extension1 Penalty for extending a short gap. Less severe than gap opening penalty. Default is 2.
-G, --gap_open2 Penalty for initiating a long gap. Aims to manage long gaps strategically. Default is 12.
-E, --gap_extension2 Penalty for extending a long gap. Provides a lenient approach to long gap management. Default is 1.
-a, --sam_output Whether to output in SAM format. If specified, results will be saved in SAM format.
-p, --paf_output Whether to output in PAF format. If specified, results will be saved in PAF format.
Note: The -r -q (input) and -o (output) parameters are required. For most users, the default settings are recommended, but feel free to adjust them as needed.
After running RaMA, the following output files will be generated in the specified output directory:
- output.fasta: Alignment results in FASTA format.
- cigar.txt: Alignment results in CIGAR format.
- reliable_region.csv: Contains information about the alignment reliability and rare matches. We define a rare match as an alignment with high reliability. Additionally, if the alignment result between rare matches consists of a simple insertion, simple deletion, or a perfect match, this interval is also considered part of the Rare Match-based Reliable Region. Example content:
cigar reliablity rare match 1178I 1 0 326= 1 1 1X 1 0 1073= 1 1 1X 1 0
- confidence: Indicates whether the alignment is considered reliable.
- rare match: Indicates if the corresponding CIGAR is a rare match.
- first_anchor.csv: Rare match anchors obtained during the first iteration.
- final_anchor.csv: All rare match anchors after the final iteration.
- intervals_need_align.csv: Regions that require wavefront alignment.
- RaMA.log: Contains information about the alignment process.
- output.sam: If the -a option is selected, the result will be saved in SAM format.
- output.paf: If the -p option is selected, the result will be saved in PAF format.
Apache 2.0 © [MALABZ_UESTC Pinglu Zhang]
RaMA is actively developed and maintained by ZOU's Lab. For any questions, feedback, or support, we encourage you to connect with us:
- Issue Tracker: For reporting bugs, suggesting enhancements, or requesting features, please use our GitHub Issues.
- Email: For direct communication, you can reach out to Pinglu Zhang at pingluzhang@outlook.com.