Data from: A fast and efficient single-stranded genomic library preparation method optimized for ancient DNA

We present a protocol to prepare extracted DNA for sequencing on the
Illumina sequencing platform that has been optimized for ancient and
degraded DNA. Our approach, the Santa Cruz Reaction or SCR, uses
directional splinted ligation of Illumina’s P5 and P7 adapters to convert
natively single-stranded DNA and heat denatured double-stranded DNA into
sequencing libraries in a single enzymatic reaction. To demonstrate its
efficacy in converting degraded DNA molecules, we prepare five ancient DNA
extracts into sequencing libraries using the SCR and two of the most
commonly used approaches for preparing degraded DNA for sequencing: BEST,
which targets and converts double-stranded DNA, and ssDNA2.0, which
targets and converts single-stranded DNA. We then compare the efficiency
with which each approach recovers unique molecules, or library complexity,
given a standard amount of DNA input. We find that the SCR consistently
outperforms the BEST protocol in recovering unique molecules and, despite
its relative simplicity to perform and low cost per library, has similar
performance to ssDNA2.0 across a wide range of DNA inputs. The SCR is a
cost- and time-efficient approach that minimizes the loss of unique
molecules and makes accessible a taxonomically, geographically, and
temporally broader sample of preserved remains for genomic analysis.