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In the section where you mention the 5 processors you used, besides the brief explanation you already give, try to add some real data examples of the data that arrives and leave each processor.
I would arrange the structure as follows:
1 Introduction
2 Preliminaries -> Here the explanation of how to create a (JS/TS) processor from scratch
3 Substring fragmentation pipeline -> Here the step by step explanation of every involved processor
I like the initial example you give of how to create a processor and I see you included some comments that mention what is the purpose of the different parts of the turtle configuration mean. Perhaps it would be better if you make those descriptions outside since at the moment they are not very visible.
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