What Is The Difference Between 'Fragment Recruitment' And 'Aligning Reads To A Reference Sequence'?

Question

[User 6228]

I have to perform 'fragment recruitment' on my metagenomic reads to generate plots of the percentage identity in the reference sequences. From what I can tell, fragment recruitment just amounts to aligning the reads to a reference sequence.

However I believe there are subtle differences in what these phrases mean that is causing me trouble. Could anyone clarify what the difference is, if there is one?

Thanks

[User 6228]

From Aleksandr's answer, I understand that 'fragment recruitment' applies specifically to metagenomic data and finding which species are represented, while 'aligning reads' applies to a broader range of read to reference sequence comparisons (for example, measuring how well a subset of mouse DNA is represented in a reference human genome)

Answer 1

[Aleksandr Levchuk]

• Aliging Short reads to a rererence and fragment recruitment are fundamentally the same method: http://gos.jcvi.org/users/gosPhaseII/AdvanceReferenceViewerDocumentation.pdf

• There is more culture around fragment recruitment term (e.g. fragment recruitment plots).

• Fragment recruitment is specifically dealing with metagenomic issues (e.g. Trying to tell apart different species).

[User 6228]

Perfect, thank you. Could you explain in more detail what you mean about 'more culture around fragment recruitment'?

[Aleksandr Levchuk]

Please see "fragment recruitment plots" in the link that I provided. By "more culture" I mean evolved methodologies like this plot. In a way Aligning Short reads is to broad of a term to have such methodologies associated with it.

[xapple]

The link you provided is 404.

[h.mon]

There is a fragment recruitment plot on this paper:

The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific