when a contig is called "orphan"?

Question

[madiha_shabbir46]

Hi there, I am struggling to get the idea of "orphan contigs", can any one help me to understand this.

It is mention in this paper http://genome.cshlp.org/content/20/10/1432 and many others.

Regards, Maidha

Answer 1

[Wietje]

I suppose "orphan contigs" simply refers to contigs that were constructed from orphan reads, i.e. reads that could not be mapped (to the reference genome). Does this help you?

[madiha_shabbir46]

Thank you wietje, it helped me to get it better, but there is one confusion. Is there any number of orphan reads in orphan contig beside normal reads? or the whole contig is just made up from orphan reads? And what if we don't have reference genome (to define orphan reads) instead Denovo assembly, where we make contigs by our self., IN that case how we define orphan reads and contigs.