ZOOM Lite: next-generation sequencing data mapping and visualization software

Abstract

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. The software is freely available at http://bioinfor.com/zoom/lite/.

Figure 1.

The main window of ZOOM Lite. (A) ‘Jobs Tree’ to organize projects user created. Each job node has two nodes. One is ‘Scheduling’ showing the mapping tasks launched for this job. The other is ‘Results’ appearing after the job is finished. (B) ‘Monitor window’ to monitor the mapping progress of jobs. (C) Overview of the read depth graph along the whole reference sequence. Multiple navigation modes are supported in this window. (D) ‘Detailed Information Window’ to show the alignment between a specific read and the reference sequence as in this figure or mapping results summary.

Figure 2.

The sequence alignment view of mapping results. The reference sequence and the assembled consensus sequence (with green background) are at the bottom of the ‘Mapping Result Illustration Window’. The mapped reads are piled along the reference sequence. Red color spotlights the differences. (A) This is an example of SOLiD data in decoded nucleotide reads mode. (B) This is the color space reads mode of the same data as in (A).