Mapping vs Alignments

2025-08-24

In bioinformatics, there are multiple programs where you need to match a sequence in one file to a sequence in a different file. I have been using these words interchangeably and apparently that is not precise enough.

It has been rather muddled in the literature as well.

Based on the presentation by Heng Li in 2011, the bioinformatician that excels in his developer skills to make programs like bwa and minimap2. He described the difference as such:

Apparently the big detail is about where the read is, do you care or not.

If you don't care, its mapping. If you do care, it's aligning.