Many high-throughput DNA sequencing methods provide very short reads, typically of a few tens of base pairs. New algorithms and softwares are needed to analysis those short reads effectively. There are some software tools for aligning short reads to a reference genome. Here we introduce a new method, Umap, to align theses short reads faster and more exact. Applying Umap to simulated very short reads generated by slicing human genome chromosome 22 into reads of length 20~100, one can identify 95% of the simulated reads' relative position. When applying to real Illumine Sequence Analyzer data sets without read pairs, Umap identify 85% of the whole reads' relative position to a Streptococcus suis genome. Umap presents a new approach to alignment short reads to reference genome quickly.
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