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This chapter introduces concepts and terminology that will be referred to in the rest of the manual. 1.1 Concepts and Terminology. Read. These resources cover key topics in next-generation sequencing (NGS) designed for beginners. We'll guide you through the workflow, tutorials, and planning +1.650.919.7300. Europe. +33.(0)1.3904.6880. Japan. +81.(0)77.565.6999. Page 1 of 43. Takara Bio USA. Cogent™ NGS. Analysis Pipeline v1.5. User Manual.Assess the overall quality of NGS sequence reads. • Visualise the quality, and other associated matrices, of reads to decide on filters and. This manual introduces the basics of aligning next generation sequence (NGS) data to reference genomes/transcriptomes using the tools available at Galaxy, Bioruptor® NGS manual. Diagenode's Bioruptor® NGS uses a gentle method of sonication to retain the integrity of DNA. The Bioruptor® Sonication System uses a Figure 3: Next-Generation Sequencing Chemistry Overview—Illumina NGS includes four steps: (A) library preparation, (B) cluster generation,(C) sequencing,