Advice on building custom sequence aligning tool for educational reasons
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8 days ago

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.

learning alignment programming Rust • 179 views
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