PERFORMANCE COMPARISON OF NEXT GENERATION SEQUENCING PLATFORMS Bekir Erguner 1,3, Duran Üstek 2, Mahmut Ş. Sağıroğlu 1 1Advanced Genomics and Bioinformatics Research Center (İGBAM), BİLGEM, The Scientific and Technological Research Council of Turkey (TUBITAK), Kocaeli, TURKEY 2Medical Genetics Department, Istanbul Medipol University, Istanbul, TURKEY 3Molecular Biology, Genetics and Bioengineering Department, Sabanci University, Istanbul, TURKEY Here we demonstrated quality and accuracy values of three of the most popular NGS platforms in a typical sequencing project. HiSeq was the most accurate sequencing platform for all quality measures. Especially it produces much fewer indels compared to other two platforms. This makes it very favorable for sequencing large genomes when its high yield and low cost are considered. The downside is its short read length which makes it less favorable for de novo sequencing and assembly projects because shorter reads produce shorter contigs. FLX produced the longest reads with base qualities comparable to HiSeq's. Researchers choose FLX for de novo sequencing project because its long reads yield longer contigs when assembled. This advantage usually outweighs accuracy disadvantage when the goal is creating the most contiguous assembled genome. IonTorrent performed poorest among the three platforms. It has the highest miscall and indel rate. Even though it is claimed that it is capable of sequencing longer reads, in our experience, many reads are too short to be used for sequencing large eukaryotic genomes. Its advantage is its quick runtime which may be crucial running routine clinical tests. © TÜBİTAK 2015 Advances in DNA sequencing technologies keep increasing the throughput while decreasing the cost. The Next Generation Sequencing (NGS) platforms use massively parallel sequencing methods to create millions, even billions of short reads at a single run with lengths ranging from 50 to 800 base pairs. This revolutionary advancement is opening up new research areas in genomic studies. Low cost and high yield of NGS platforms are making them attractive for researchers. They are also being adopted for clinical applications since recently. For researchers and clinicians who are planning to adopt these platforms, one of the main questions is their sequencing accuracy. Here we compare sequencing performance of three of the most commonly used NGS platforms; Ion Torrent from Life Technologies, GS FLX+ from Roche and HiSeq 2000 from Illumina. Each platform has its own strengths. HiSeq has the highest throughput, IonTorrent is the fastest, and FLX gives the longest reads. While each system has its merits for users to select it, we will focus on their data quality and sequencing accuracy in this study. We sequenced a BAC plasmid clone carrying 177,000 bp long piece of human chromosome 13 with very high depth of coverage with each platform. We will compare read lengths, overall base-calling accuracy and system specific sequencing errors. Figure 1. Base quality of platforms relative to base positions in short reads. Plots created by FastQC. Table 1. General information about the data IEEE EMBC August , Milan, Italy Roche 454 GS FLX+Ion TorrentIlumina HiSeq 2000 Number of reads711,4283,348,883111,137,282 Number of bases383,299,699270,223,63910,382,101,649 Amount of bases with QS>= %35.4%92.5% Avg. read length Amount of aligned reads91.7%89.9%98.5%