ZOOM

ZOOM maps short sequencing reads generated by Illumina/Solexa technologies to the human reference genome using a spaced-seed framework to provide rapid, fully sensitive alignments for resequencing and variant detection.

Key Features:

• Efficient mapping framework: Uses a spaced-seed framework to achieve full sensitivity in read mapping.
• High throughput: Maps 15× coverage of the human genome within one CPU-day and can process billions of short reads per day.
• Mismatch tolerance: Allows up to two mismatches while maintaining full sensitivity for accurate alignment in the presence of sequencing errors or genetic variation.
• Computational optimization: Optimized to run on standard computational resources to accelerate large-scale short-read mapping.

Scientific Applications:

• SNP discovery: Facilitates identification of single nucleotide polymorphisms (SNPs) from deep sequencing data.
• Rare transcript detection: Enables detection of rare transcripts from high-coverage Illumina/Solexa datasets.
• Resequencing and personalized medicine: Supports human genome resequencing projects and analyses relevant to personalized medicine.

Methodology:

ZOOM employs a spaced-seed approach using patterns of fixed-length seeds with gaps to quickly identify potential matches in the reference genome while accommodating mismatches.