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The use of digital tools has revolutionized academic research in the humanities, changing its approaches, methodologies and outcomes. The phenomenon is comparable to the radical change induced by the introduction of printing and has created a new interdisciplinary area called digital humanities or humanities computing. The application of humanities computing to the study of early Qurʾānic manuscripts can affect the access to and comprehension of these objects in three main aspects. Digital tools change, first, our access to illegible objects through digital images and, second, our editing of manuscript texts by means of tagging systems that produce a structured and searchable/processable archive of the information that manuscripts contain. Last, information technology borrowed from DNA-sequencing tools in biology can be applied to manuscript studies for the encoding of multiple manuscripts and facilitates our understanding by suggesting possible connections between manuscripts. The paper will discuss the methodological innovations - in terms of imaging processing, tagging of text and phylogenetics - of research projects that have already been carried out and the feasibility of establishing a collaborative space for annotating Qurʾānic manuscripts, taking into consideration actors, audiences and purposes.