Which current method do you recommend for evaluating whole-genome sequence data at a resolution of individual nucleotides and saving the results as a number array that can be processed via NumPy or R? Take, for example, the objective of identifying and indexing the position of all G and C nucleotides on a particular chromosome to measure local GC compositional heterogeneity and identify new CpG islands.

In the past, I would conduct such analyses via the Python library 'Plastid' (https://doi.org/10.1186/s12864-016-3278-x) but it does not appear to be maintained any longer and fails upon installation. Thus, I am looking for alternative methods.