mkESA

mkESA constructs enhanced suffix arrays (ESAs) from biological sequence data to enable efficient indexing and string-matching operations.

Key Features:

• Algorithmic Foundation: Parallelized implementation of Manzini's lightweight Deep-Shallow suffix array construction algorithm for ESA construction.
• Parallel Processing: Utilizes multiple CPUs/cores to accelerate suffix array and ESA construction on large datasets.
• Outputs: Produces enhanced suffix arrays and additional tables including the LCP (Longest Common Prefix) table and the inverse suffix array.
• Compatibility: Generates output compatible with mkvtree from the Vmatch package.
• Implementation: Implemented in portable C99.

Scientific Applications:

• Large-scale sequence indexing: Construction of ESAs from large FASTA files containing multiple sequences for downstream analyses.
• Genome assembly: Provides suffix-array-based data structures used in analyses related to genome assembly.
• Sequence alignment: Facilitates substring searches and alignment-related tasks via the inverse suffix array and LCP table.
• Pattern searching: Enables efficient string matching and pattern detection in genomic sequences using suffix arrays and LCP information.

Methodology:

Parallelized Manzini lightweight Deep-Shallow suffix array construction algorithm implemented in portable C99 to build enhanced suffix arrays and compute LCP and inverse suffix arrays.