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?
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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).
Perfect, thank you. Could you explain in more detail what you mean about 'more culture around fragment recruitment'?
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.
There is a fragment recruitment plot on this paper:
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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)