Approximate local alignment via chained MEM divergence estimation for detecting horizontal gene transfer
Local alignment tools struggle at querying against thousands of bacterial genomes, because the reference indexes are memory-intensive and base-level dynamic programming is slow. We present alamem (https://github.com/yunwilliamyu/alamem), an approximate local aligner that streams unprocessed reference databases and estimates average nucleotide identity (ANI) from Maximal-Exact-Match (MEM) chaining…
We haven't written up this one. bioRxiv has the full story — the link below goes straight to it.
