Aligner (based on vsearch)

[MatthewRalston]

I'm trying to juggle the aligner and the assembler in 2024. The aligner revolves around k-mer match numbers and their scoring to prioritize alienable sequences. The database .fasta would be processed first, as is typical in most aligners. Your database is typically larger, and contains exact sequences for the transcripts, CDSes, or target genomic sequences. Your query sequences are also fasta format. Doing it in one step later down the road would be a good goal? But it's not essential algorithmically speaking.