The quality of Ion Torrent is more stable, while the quality of HiSeq 2000 decreases noticeably after 50 cycles, which may be caused by the decay of fluorescent signal with increasing the read length (shown in Figure 1).

10.5.1.1 MAPPING

The insert size of library of Rhodobacter was 350 bp, and 0.5 Gb data was obtained from HiSeq. The sequencing depth was over 100x, and the contig and scaffold N50 were 39530 bp and 194344 bp, respectively. Based on the assembly result, we used 33 Mb which is obtained from ion torrent with 314 chip to analyze the map rate. The alignment comparison is Table 2.

The map rate of Ion Torrent is higher than HiSeq 2000, but it is in­comparable because of the different alignment methods used in different sequencers. Besides the significant difference on data including mismatch rate, insertion rate, and deletion rate, HiSeq 2000 and Ion Torrent were still incomparable because of the different sequencing principles. For example, the polynucleotide site could not be indentified easily in Ion Torrent. But it is shown that Ion Torrent has a stable quality along sequencing reads and a good performance on mismatch accuracies, but rather a bias in detection of indels. Different types of accuracy are analyzed and shown in Figure 1.