PgSA

PgSA indexes and queries collections of next-generation sequencing (NGS) reads in main memory to count and locate k-mers using a pseudogenome suffix array.

Key Features:

• Efficient Indexing: Constructs an index based on a pseudogenome suffix array optimized for space usage and query performance.
• K-mer counting and locating: Supports counting and locating k-mers within sequencing reads.
• Memory Optimization: Operates in main memory to reduce disk I/O when processing large read collections.
• Interface compatibility: Adheres to the interface proposed by Philippe et al.

Scientific Applications:

• Variant Calling: Identifies genetic variants by analyzing k-mer patterns within sequencing reads.
• Error Correction: Detects and helps correct sequencing errors by locating discrepant k-mers.
• RNA-seq Analysis: Processes RNA-seq reads to support analysis of gene expression patterns and transcriptomic variation.

Methodology:

Constructs a pseudogenome suffix array that captures overlapping reads and uses it to count and locate k-mers in main memory, adhering to the interface proposed by Philippe et al.