I'm a happy user of the DNABarcodes package by Tilo Buschmann. I came across the paper by Hawkins, John A., Stephen K. Jones, Ilya J. Finkelstein, and William H. Press. 2018. “Indel-Correcting DNA Barcodes for High-Throughput Sequencing.” Proceedings of the National Academy of Sciences 115 (27): E6217–26. https://doi.org/10.1073/pnas.1802640115 where they state that
... but an error in the derivation of these codes [Buschmann & Bystrykh 2013] often causes the decode spheres to overlap, resulting in wrong barcode decodings (SI Appendix) ...
Buschmann & Bystrykh 2013 is the paper on which the DNABarcode package is based. I coudn't quite follow the argument but does anyone know if this (still) the case? And if so, under which circumstances?
Regards,
Philip
Hi Phillip -- I was wondering if you came across this again. Im digging into the barcode space, and wondering if it's advisable to use the methods presented in Hawkins et al, vs the DNABarcode package.
When reading the paper, I started to interpret as if you use the DNABarcodes package to generate barcodes, but then use a different method for decoding it could run into an issue. Unsure if that is an accurate take.