spades VS sage

If you do DNA sequencing and receive the sequencing files as fastq files (normal from sequencing) then spades to assemble the genome, then put it through PROKKA to annotate it. Here's a beginners guide, the most difficult part is downloading the programs onto your laptop.

MetaSpades has a cool option to hybrid reform contigs using short and long reads so you could pair short read data and long read data (PacBio/ONT) to get the best hybrid assembly with high throughput and long reference reads for resolving the reassembling. https://github.com/ablab/spades

If you want to implement LDA from scratch, you could check out how Sage is doing it.

You could check out https://github.com/lazear/sage - it's a near comprehensive program/pipeline for analyzing DDA/shotgun proteomics data. Most proteomics pipelines consist of running multiple, separate tools in sequence (search, spectrum rescoring, retention time prediction, quantification), but sage performs all of these. This cuts down on the need for disk space for storing intermediate results (none required), the need for IO (files are read once), and results in a proteomics pipeline that is >10-1000x faster than anything else, including commercial solutions

You can also check out the intro blog post if you're interesting in learning more about the algorithm behind Sage. Beyond being fast, it also includes integrated machine learning (linear discriminant analysis, KDE) for rescoring spectral matches.

You could try out Sage, if you're looking for speed - I don't think you'll find anything faster. https://github.com/lazear/sage