Review of Recent Ngs Short Reads Alignment Tools Bmi-231 Final Project, Chenxi Chen Spring 2014

Deciphering the information contained in DNA sequences began decades ago since the time of Sanger sequencing. The development of next generation sequencing makes it possible to study organisms on the genome scale. NGS have been used in various types of studies including genome re-sequencing (DNA-seq), DNA-protein interactions (ChIP-seq), transcriptom reconstruction, quantitative analysis (RNA-seq) and so on. As the improved efficiency of sequencing technologies such as PacBio RS II, Ion Torrent proton and Illumina HiSeq X Ten, sequencing price has dramatically dropped to as low as $1,000 for sequencing a human genome, which facilitates the rapid raising of data generating. Correct data interpretation is urgently needed. Aligning short reads to reference genome with sufficient quality is a prerequisite for many comparative genomic studies. Variant types of software are available for short reads alignment. This review will focus on discussing the most commonly used aligners in recent 2-3 years.