Dr. Adam Rosenthal, a professor in the Department of Microbiology and Immunology at UNC Chapel Hill, performed a study comparing the speed and accuracy of whole plasmid sequencing services across five top providers using blinded, real-world samples. Across 42 submitted plasmids, including samples with low concentration, degraded DNA, or challenging sequences, Plasmidsaurus stood out, outperforming all other vendors on both quality and speed.
Thirteen unique plasmid sequences were submitted at a range of concentrations to total the 42 experimental conditions. Plasmids ranged in length from 3-8 kb, with concentrations between 0.5 ng/μl and 50 ng/μl, and were selected to represent challenging real-world scenarios including highly repetitive sequences, multimers, degraded DNA, and mixed populations with multiple plasmid sequences present.
To compare different sequencing services, both quality and speed were assessed. Returned consensus sequences were aligned to the known ground-truth sequence to determine accuracy. In cases where the result did not perfectly match the reference sequence, the type of error was recorded.
Different types of sequencing errors can have dramatically different impacts on research conclusions. We categorized four kinds of error:
- Assembly errors: Misassembly of contigs leading to rearranged, truncated, or chimeric plasmid sequences.
- Homopolymer or methylation-associated errors: Ambiguities in repetitive regions or methylated bases that can occur with Nanopore long-read sequencing (you can learn more about common errors and what we do to mitigate them here).
- Mismatches: Other incorrect base calls or small insertions or deletions causing the result to differ from the true plasmid sequence.
- Fail: No sequence returned.
On these 42 complex sequences and difficult samples, Plasmidsaurus performed the best, returning a perfect match to the reference sequence significantly more often than other vendors, with just one failed sequence and three samples with homopolymer or methylation errors. Other vendors returned dramatically more errors across the samples sequenced, including many plasmid assemblies with mismatches and assembly errors that can derail research progress. These errors were more pronounced at lower concentrations, with some vendors unable to return any error-free assemblies at the lowest concentrations tested.
Turnaround times were measured from when vendors notified Dr. Rosenthal that samples had been received. Plasmidsaurus returned results four hours after arrival of the samples in the lab, up to six times faster than other vendors.
At Plasmidsaurus, our mission is to accelerate biologists with the best tools possible. We’re grateful to Dr. Rosenthal for his study validating the hard work we do to keep researchers moving forward. Ready to start sequencing? Check out Whole Plasmid Sequencing options here.