ZOOM Lite

ZOOM Lite is a next-generation sequencing data mapping and visualization software. Users input reference genomes and Illumina/Solexa short reads files or AB SOLiD color space reads files in various formats, such as *.fasta, *.fastq, *_seq.txt, *.csfasta etc. ZOOM outputs the mapping results of these short reads on the reference sequence. ZOOM Lite has a fast and accurate mapping kernel based on a newly designed multiple spaced seeds theory. Both single-end and paired-end reads of various lengths from 15bp to 240bp can be handled. Any number of mismatches and one insertion/deletion of various lengths between the read and its target region on the reference sequence are allowed. Uniquely mapped results or best (top N) results for each read will be reported according to the minimal mismatches and indel length. Quality scores are utilized to enhance mapping accuracy. Based on the mapping kernel, ZOOM Lite allows users to load local read data and reference sequence data, select proper parameters, process high volume data in parallel among up to four CPUs, monitor the running tasks, store the mapping results, view the graphs of mapping results and output mapping results in either *.BED or *.GFF file formats for further surveying with the UCSC browser track information. Mapping results can be viewed in any desired scale, from the read depth graph over an entire chromosome to detailed sequence alignments between reads and the reference sequence. Users easily navigate to regions of interest simply via click and drag or scrolling. ZOOM Lite is a derivative of the ZOOM Studio software.