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Illumina, PacBio and Oxford Nanopore: Customized Data Analysis and Interpretation

These days, many tools have been developed for next-gen sequencing (NGS) data processing and analysis, and there are many cloud-based systems that allow you to run various bioinformatics tasks without having to write a single line of code. Moreover, newer sequencing platforms, such as Pacific Biosciences (PacBio) and Oxford Nanopore (ONT), have even developed “hands-free” data analysis solutions, i.e., they have integrated the data analysis systems into their data collection systems. Who in the world still needs to hire professional bioinformaticians to do data analysis work?

In fact, it is the view of many professional bioinformaticians that cloud-based integrated analysis systems and “hands-free” solutions offered by PacBio and ONT do more harm than good by giving a false sense of easiness to lay users. Illumina, PacBio and ONT are new and very fast-evolving technologies. Handling data generated in these platforms could be very tricky. Most bioinformatics experts agree that except for the simplest situations with the most straightforward tasks and most ideal data, analysis and interpretation of Illumina, PacBio and ONT data could not be done optimally using existing tools without careful tuning and/or some level of customized coding. Even simple tasks such as read alignment and sequence assembly could turn out to be much more involved than what you imagined, let alone more advanced research problems which require that the best information be extracted from the costly and hard-earned data.

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