Next Generation Sequencing. Since Xxxxxxxxx Xxxxxx developed the chain-termination based DNA sequencing tech- nology in 1977, it has been selected as the principle technology for the “first gener- ation” laboratory and commercial sequencing applications for nearly three decades [1, 2]. After years of improvement and automation, Sanger sequencing technology became the major tool for the completion of the human genome project (HGP) [3] which cost about $2.7 billion and involved 18 countries during 11 years. This project published progressively improved versions of human reference genomic assembly (hg4∼hg15) in FASTA format (xxxx://xx.xxxxxxxxx.xxx/wiki/FASTA_format). Although HGP was completed, the developing of human reference genome is still continuing. The latest version is hg38 which was published for downloading on UCSC website in December 2013 (xxxxx://xxxxxx.xxxx.xxx). Not long after HGP was completed in 2003, Next Generation Sequencing (NGS) technologies were published in 2005 [4]. These new technologies, in contrast to its predecessor, are low-cost high-throughput sequencing technologies which massively parallelize sequencing analysis. Therefore, NGS is also called Massively Parallel Sequencing (MPS). It is practically supplanting the Sanger sequencing due to its ultra-high sequencing speed and ultra-low cost [5]. Since the emergence of NGS, the price dropping pattern of DNA sequencing has been more remarkable than that in Xxxxx’x Law [6]. SOLiD/Xxx Xxxxxxx PGM from Life Sciences, Genome Analyzer/HiSeq 2000/MiSeq from Illumina, and 454/GS FLX Titanium/GS Junior from Roche are the major NGS sequencer platforms and commercial vendors. Those platforms can generate millions of reads in a single run within hours. The output reads types can be DNA-seq [7], RNA-seq [8, 9], ChIP-Seq [10] or BS-Seq [11]. The length of generated reads ranges from 30 base pairs (bp) to 400 bp [12] , usually stored in a de facto standard FASTQ format [13] or Sequence Read Archive (SRA) format [14] from National Center for Biotechnology Information (NCBI). Reads can be single-ended or paired-ended, and they can be tagged as from sense strand, antisense strand or unknown strand. NGS’s high-throughput power has been harnessed by many researchers to inves- tigate and solve genetical, genomical and clinical problems [8, 15–19]. Despite their diverse and wide range of categories and applications, most of them share a crucial problem: how to correctly and efficiently identify the genomic locations (chromo- some,...
