This repository implements a memory-efficient method for direct sparse suffix array (SSA) construction using the Libsais library. Unlike traditional approaches that first build a full suffix array before sampling, this method directly constructs the SSA through a simple text transformation. By encoding groups of k characters into compact integer representations, the memory usage reduces significantly.
Key Benefits:
- Lower memory usage (no need for a full suffix array)
- Faster SSA construction (directly processes transformed text)
- Optimized for bioinformatics
How It Works:
- Bit-pack characters into compact integers while preserving lexicographic order.
- Use Libsais to construct the suffix array of the transformed text.
- Achieve direct SSA construction, avoiding unnecessary memory overhead.
Clone the repository and build the executable:
git clone [email protected]:unipept/unipept-libsais.git
cd unipept-libsais
mkdir build && cd build
cmake ..
make
This will generate the build_ssa executable.
Run the program with the following syntax:
./build_ssa -s <sparseness> [-cdo] <input_file> <output_file>
- -s : Defines the sparseness factor (an integer).
- -d: Treats the input file as DNA data (default assumes proteomic data).
- -c: Enables compressed output using bit-packing.
- -o: Uses the optimized algorithm for faster processing.
- <input_file>: Path to the input file containing DNA/protein sequences.
- <output_file>: Path where the sparse suffix array will be saved.
./build_ssa -s 3 -o input.txt output.ssa
This command builds an SSA with sparseness factor 3, treats the input as proteomic data, and uses the optimized algorithm.
This tool contains a modified fork of the libsais library. The libsais library is a tool for fast linear time suffix array based on induced sorting algorithm described in the following papers:
- Ge Nong, Sen Zhang, Wai Hong Chan Two Efficient Algorithms for Linear Suffix Array Construction, 2009
- Juha Karkkainen, Giovanni Manzini, Simon J. Puglisi Permuted Longest-Common-Prefix Array, 2009
- Nataliya Timoshevskaya, Wu-chun Feng SAIS-OPT: On the characterization and optimization of the SA-IS algorithm for suffix array construction, 2014
- Jing Yi Xie, Ge Nong, Bin Lao, Wentao Xu Scalable Suffix Sorting on a Multicore Machine, 2020
Original Copyright (c) 2021-2024 Ilya Grebnov [email protected]
The libsais is inspired by libdivsufsort, sais libraries by Yuta Mori and msufsort by Michael Maniscalco.
- Removed functionality for computing the Burrows-Wheeler transform and longest common prefix array.
- Removed OpenMP acceleration.
- Removed construction of a 32-bit suffix array.
- Added functionality for contstructing a 64-bit suffix array for a 32-bit input.
Unipept-libsais is released under the Apache License Version 2.0