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As far as I can tell, there is no noticeable difference between the tags read-mapping and alignment. Three of the fifteen questions under these two tags use both tags, and the rest seem too similar to warrant any separation.

EDIT: Clearly I had failed to notice the quite significant difference between these terms. However, the ambiguity of the alignment tag and the way in which it is being used should be fixed. Terdon's answer below gives a good resolution of this issue.

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No! When I hear "alignment" I will immediately think of protein or nucleotide multiple sequence alignments. I mean what is done by tools like t_coffee, mafft, clustal etc. That's what the word always meant when I started working in bioinformatics and I am sure I am not alone. Not everyone works in NGS analyses, you know :)

I would instead argue that precisely because the term alignment is not specific and can apply to many things, we should instead make more focused tags. So, we should have:

The is a classic meta tag since there is no way of knowing what type of alignment it is describing without an additional tag to clarify. it should therefore be removed and not used at all.

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That's fine until someone wants to make salmon or kallisto-specific questions, since there the distinction between mapping and alignment is clear.

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  • $\begingroup$ I’m not even sure I’d call Salmon etc. mapping tools; rather, they’re alignment-free quantification tools. But it’s certainly true that kmer-based identification (or similar methods) is mapping, yet not necessarily alignment. $\endgroup$ – Konrad Rudolph Jun 14 '17 at 12:46
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I think these tags are two different things. Reads mapping refers to a process when sequencing to find the position of a read to a reference genome while alignment is comparing two (or more) sequences.

Both can be DNA, but one can align also proteins, but I haven't heard of read-mapping proteins. For instance one can align some orthologous or paralogus genes/proteins which don't need to be reads.

That said, the excerpts should make clear the distinction (if the community agrees with this) to facilitate the usage of the right tag.

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