Overview

ZOOM (Zillions Of Oligos Mapped) is designed to map millions of short reads, emerged by next-generation sequencing technology, back to the reference genomes, and carry out post-analysis. ZOOM is developed to be highly accurate, flexible, and user-friendly with speed being a critical priority.

ZOOM is fast. A single CPU with only 6.5G of memory is capable of mapping 15X coverage of a human genome in one day using ZOOM at full sensitivity while tolerating two mismatches.

ZOOM is accurate. The spaced seed strategy specially extended for short reads mapping problem guarantees 100% sensitivity for a wide range of read length and mismatch numbers. Tests on benchmarks also show great accuracy with the present of insertions and deletions.

ZOOM is flexible:

• Supports Illumina/Solexa and ABI SOLiD instruments
• Easily maps reads 15 to 240 bps long (NEW!)
• Handles both mismatches and insertions/deletions
• Supports paired-end reads mapping
• Assess alignment probability using read sequence quality scores (NEW!)
• Reports uniquely mapping results or best N mapping results for each read
• Integrated multiple sequence alignment for consensus reconstruction and SNP identification.
• Coverage and heterozygous information for each position of consensus sequence reported.
• Automatically detect and correct sequencing errors for ABI SOLiD data
• Decode reads in color space into base space, with sequencing errors and polymorphisms highlighted.

ZOOM is Scalable. Time complexity increases approximately linearly with respect to genome length and reads number.

False positives problem? ZOOM increases uniquely mapped reads with quality score and paired end statistics. This reduces ambiguity of read mapping and increase the likelihood of identification