In recent years, a large number of mapping algorithms have been developed for read mapping and RNA-Seq differential analysis [ 9- 14].
He began his career cracking Japanese military codes during the second world war, then developed machines for reading written text.
Many computational tools have been developed for separating reads from different species or groups of related species (we will refer to the problem as the clustering of reads).
At our last enumeration, 24 academic de novo genome assemblers, each possessing its own range of application, are developed for short reads datasets from different sequencing platforms in the last few years.
Both HGAP and AHA are specifically developed for PacBio reads and can fix potential sequencing error.
Trinity [ 12] in contrast is a de-Bruijn graph-based assembler developed for short reads.
Although a serial pyrosequencing technique using multiple primers has been developed for extended read lengths, it is still constrained by short PCR amplicon lengths [ 14].
Many de novo assemblers utilizing the de Bruijn graph-based approach were developed for NGS reads, such as Velvet, SOAPdenovo, ALLPATHS, Edena, EULER-SR, and EULER-USR [ 8– 14].
Numerous methods have been developed for short read alignment including Maq (Li,H. et al., 2008), BowTie (Langmead et al., 2009), ELAND (Illumina), SHRiMP (Rumble et al., 2009), BWA (Li and Durbin, 2009), SOAP (Li,R. et al., 2008) and Mosaik (http://bioinformatics.bc.edu/marthlab/Mosaik).bc.edu/marthlab/Mosaik
Various such alignment tools or pipelines have been developed for detecting spliced reads in short read data within local regions of a genome, including QPALMA [ 24] and TopHat [ 25].
