Our Research

Here is a collection of the main research conducted during the development of the ZOOM software.

BSI Published Research Zhang Z, Lin H, Ma B. ZOOM Lite: next-generation sequencing data mapping and visualization software. Nucleic Acids Res. 2010 Jun 8.
High-throughput next-generation sequencing technologies pose increasing demands on the efficiency, accuracy and usability of data analysis software. In this article, we present ZOOM Lite, a software for efficient reads mapping and result visualization. With a kernel capable of mapping tens of millions of Illumina or AB SOLiD sequencing reads efficiently and accurately, and an intuitive graphical user interface, ZOOM Lite integrates reads mapping and result visualization into a easy to use pipeline on desktop PC. The software handles both single-end and paired-end reads, and can output both the unique mapping result or the top N mapping results for each read. Additionally, the software takes a variety of input file formats and outputs to several commonly used result formats.
BSI Published Research Lin H, Zhang Z, Zhang MQ, Ma B, Li M. ZOOM! Zillions of oligos mapped. Bioinformatics. 2008 Nov 1;24(21):2431-7.
MOTIVATION: The next generation sequencing technologies are generating billions of short reads daily. Resequencing and personalized medicine need much faster software to map these deep sequencing reads to a reference genome, to identify SNPs or rare transcripts. RESULTS: We present a framework for how full sensitivity mapping can be done in the most efficient way, via spaced seeds. Using the framework, we have developed software called ZOOM, which is able to map the Illumina/Solexa reads of 15x coverage of a human genome to the reference human genome in one CPU-day, allowing two mismatches, at full sensitivity.