Noob question: semantics between terms

[dent]

I'm unsure of the difference between read mapping and contig realignment.

I've seen read mapping being described as putting reads together to form contigs, but have also seen it being described as putting reads together against a reference genome to form a draft genome. This second description is what I think contig (re)alignment describes.

Are they interchangeable?

Thank you!

[GSviral]

For me, I would interpret read mapping as aligning (or mapping) the reads against a reference genome. Putting the reads together to form contigs would be an assembly.

Contig alignment, to me, would be the same idea. Just mapping the contigs to a reference instead of the raw reads.

[dent]

For me, I would interpret read mapping as aligning (or mapping) the reads against a reference genome. Putting the reads together to form contigs would be an assembly.

Contig alignment, to me, would be the same idea. Just mapping the contigs to a reference instead of the raw reads.

so they're interchangeable to you? is it generally used interchangeably in the field?

[GSviral]

For mapping and alignment I would consider them interchangeable with regards to a reference genome, yeah. If I mentioned either to my colleagues they would understand both just the same. Just the input in your scenario is different - raw reads vs. assembled contigs. Hope this helps!