Illumina

SOLiD and 454 are three widly used platforms for the second generation sequencing.Among them

both Illumina and SOLiD rely on the polymerase chain reaction（PCR） technique

while 454 relies on the DNA ligase.When dealing with the data produced by the platform

two steps are needed:（1） the preprocess of the high throughput data;（2） sequence alignment.Generally

there are two kinds of preprocessing methods: hash table method and the method based on suffix trie of the Burrows-Wheeler transform.And there are two ways of sequence alignment: spaced seed indexing and the Smith-Waterman algorithm based on dynamic programming strategy.This paper chooses to evaluate several commonly used ones

such as: SHRiMP

MAQ

BFAST

BWA

and BOWTIE

by using two kinds of data produced by Illumina and SOLiD respectively.The results show that BOWTIE fits for aligning the sequences produced by Illumina in terms of the memory usage

speed and accuracy

while BWA suits for aligning sequences from SOLiD.Considering the situation of disharmony between processing speed and data volume produced by the second generation sequencing platforms or even the third generation sequencing platforms represented by Nanoporous

the paper suggests that new sequence alignment methods based on the cloud computing is an important direction of the future research.