Hi I am learning the rust language through developing my own bioinformatics tools to better understand how they work. I have done an implementation of Needleman-Wunsch in rust so far, but I am wondering what a relatively simple yet effective algorithm for me to replicate would be if I want to aligning reads to a reference genome. I considered Using my NW algorithm iteratively to align reads to a genome and only applying it to small viral genomes, but would that still be to computationally complex? If you have any suggestions for a logical step to take if I want to progress after building a NW and build a full alignment tool that can run in a reasonable amount of time outputting a SAM I would really appreciate it. Maybe build an index tree of some kind?
Any project ideas or pointers toward resources would be great.