Description
Hello,
Thank you for developing and maintaining Pheniqs, I'm excited to try it in a number of data processing workflows. Would you be able to provide some pointers on how/if Pheniqs's PAMLD decoder could be used for very large barcoding spaces, of 2-3 Billion barcodes. I'm working with a dataset with an 18 base barcode with a small amount of non-permitted sequences (no homopolymers longer than 5 bases). This is more akin to a random UMI sequence than the smaller whitelists of barcodes used in the use examples in this repo. The Pheniqs2.0 paper describes the intractability of very large initial whitelists, and mentions that other strategies should be considered for an initial first pass through the data to reduce the barcode space. Are there any approaches or tools which you have found to work well for these scenarios? Let me know if I can provide any more information about my particular use case.
Thanks,
Derek