Ultraplex

Ultraplex is a software tool for demultiplexing raw sequencing data from next-generation sequencing experiments. It efficiently splits raw FASTQ files containing sample-specific barcodes into separate files, a crucial first step in most sequencing data analysis pipelines. Ultraplex stands out for its ability to handle both single-end and paired-end sequencing data and its support for combinatorial barcodes located at either one or both ends of the reads.

In addition to demultiplexing, Ultraplex performs essential preprocessing tasks such as trimming sequencing adaptors and low-quality bases. It also moves unique molecular identifiers (UMIs) into the read headers, facilitating the removal of PCR duplicates in downstream analysis.

A key advantage of Ultraplex is its computational efficiency. It can process an entire Illumina HiSeq lane, containing nearly 500 million reads, in under 20 minutes. This speed and flexibility in handling various barcoding strategies make Ultraplex particularly well-suited for processing complex sequencing libraries, such as those generated by CLIP and ribosome profiling protocols.