Ultraplex

Ultraplex demultiplexes FASTQ reads by splitting raw Illumina sequencing data using sample-specific and combinatorial barcodes to prepare datasets for downstream NGS analyses.

Key Features:

• Flexibility in demultiplexing: Supports barcodes located at a single end or at both the 5' and 3' ends of reads in FASTQ files.
• Adaptor trimming and quality control: Trims sequencing adaptors and removes low-quality bases to retain high-quality reads.
• UMI handling: Moves unique molecular identifiers (UMIs) into the read header to facilitate PCR duplicate removal and molecular quantification.
• High-throughput processing: Capable of processing an Illumina HiSeq lane (~500 million reads) in under 20 minutes.
• Compatibility with sequencing types: Supports both single-end and paired-end sequencing data.
• Combinatorial barcode support: Efficiently handles combinatorial barcodes for complex sequencing libraries.

Scientific Applications:

• ChIP-seq: Processes complex ChIP-seq libraries that use combinatorial barcodes and UMIs for high-throughput demultiplexing.
• CLIP: Demultiplexes CLIP sequencing libraries that incorporate combinatorial barcodes and UMIs.
• Ribosome profiling: Handles ribosome profiling libraries requiring combinatorial barcode and UMI management.

Methodology:

Integrates barcode recognition, adaptor trimming, quality-control filtering, and UMI handling (including moving UMIs into read headers) to demultiplex FASTQ reads with barcodes at single ends or both 5' and 3' positions.