TAPyR

TAPyR aligns pyrosequencing reads generated by the GS FLX (454) system to reference genomes for high-throughput re-sequencing and downstream analyses.

Key Features:

• Burrows-Wheeler Transform (BWT)-based alignment: employs a BWT-based approach to perform efficient read alignment against reference genomes.
• Advanced indexing techniques: integrates state-of-the-art indexing to increase alignment speed and accuracy for large datasets.
• Flexible seed-based alignment: utilizes a seed-based strategy to initiate alignments accommodating variable read lengths and pyrosequencing error profiles.
• Pyrosequencing-specific optimization: optimizes local alignment accuracy and computational efficiency for pyrosequencing data from the GS FLX (454) system.

Scientific Applications:

• Re-sequencing: mapping GS FLX (454) pyrosequencing reads to reference genomes for variant detection in re-sequencing projects.
• Variant detection: enabling identification of genomic variants from mapped pyrosequencing reads.
• Gene expression analysis: aligning pyrosequencing-derived reads for transcript quantification and expression studies.
• Comparative genomics: supporting genome comparisons using mapped pyrosequencing reads from 454 sequencing.

Methodology:

Combines Burrows-Wheeler Transform (BWT)-based indexing with a flexible seed-based alignment strategy and pyrosequencing-specific optimizations to improve local alignment accuracy and computational efficiency.