gsufsort

gsufsort constructs suffix arrays, longest common prefix (LCP) arrays, Burrows-Wheeler Transforms (BWT), and document arrays from collections of sequences to enable efficient indexing, pattern matching, and data compression in bioinformatics.

Key Features:

• Efficiency: Constructs suffix arrays and related data structures in linear time O(N), where N is the number of symbols in the input.
• Algorithmic Foundation: Implements the gSACA-K algorithm for fast construction of suffix arrays from string collections.
• Portability and Lightweight Design: Written in ANSI/C for portability across platforms.
• Support for Multiple File Formats: Accepts large input files in FASTA, FASTQ, and plain text formats.

Scientific Applications:

• Genome Assembly: Managing and indexing large genomic datasets to support assembly processes.
• Sequence Alignment: Enabling efficient sequence comparison and alignment via indexed string collections.
• Data Compression and Retrieval: Using BWT for data compression and efficient retrieval operations.

Methodology:

Uses the gSACA-K algorithm to construct suffix arrays in O(N) time and generates LCP arrays, Burrows-Wheeler Transforms (BWT), and document arrays from input string collections.