In contrast, some sequence alignment tools, such as CLUSTALW [40], TBA [41], MAVID [42], MLAGAN [43], Pecan [44], Seq-SNPing [45], AQUA [46], and Cgaln [47], were developed without a primer design function.
For reads longer than 1024bp, we would explore some specific alignment tools in future, such as BWA-SW [ 37].
This algorithm can be used in the parallelization of some multiple sequence alignment tools, such as MAFFT and MUSCLE.
It is noteworthy that support for the ABI SOLiD platform has been dropped in recent versions of some of the alignment tools (e.g. BWA > 1.6.0, Bowtie2).
Some widely used local alignment tools, such as BLAST [ 68] and BLAT [ 51], are not optimal for mapping small RNAs due to their heuristics.
The k-mers counting method was implemented in some important multiple sequences alignment tools, such as MAFFT [ 6, 7] and MUSCLE [ 1], and to the extent of our knowledge there is no other work in the literature that has developed and tested a parallel approach, specifically of this method.
We analyse the problem of parallel alignment and review the parallelisation strategies of some of the most popular alignment tools (such as Bowtie and BWA), which can all be abstracted by the farm paradigm (a.k.a. master-worker or task- farm) [ 1, 2].
Reads can then be aligned using existing SOLiD alignment tools.
Although automatic alignment tools exist in some software, the accuracy of the alignment should be carefully evaluated and manual adjustment may be needed.
