https://github.com/ulelab/ultraplex
Should I use Ultraplex?
Ultraplex is primarily designed for the demultiplexing of sequencing data generated using in-house library preparation protocols, with custom adaptors (for example iCLIP libraries). If instead you are using a commercial library prep kit (eg Illumina Truseq or Lexogen Quantseq) then in all likelihood the sequencing facility will already have demultiplexed the files for you, so Ultraplex is probably not for you. Furthermore, if you are doing single cell RNA-seq or using, for example, Oxford Nanopore long-read sequencing, there are other softwares specifically designed for these purposes.