Why Is There A Sequence With Name ">Hs37D5" In The Reference Hs37D5.Fa File Of Gatk Resource

Question

[Griffan]

What is this sequence? It looks strange with such a recursion.

Answer 1

[Devon Ryan]

From the README file, it's "the concatenated decoy sequences," which would explain why it's just one contig. BTW, it's equivalent to the hs37d5cs.fa.gz file, if you're curious. If you're wondering where all of the sequences map, have a look at the various hs37d5ss.X files. Also, have a look at this blog post for some context surrounding the whole decoy genome thing (see also the pdf file from Heng Li, showing the benefits to using a decoy genome).