Flexbar

Flexbar processes and trims sequence tags from next-generation sequencing (NGS) reads to enable accurate demultiplexing, adapter and barcode removal, and improved downstream read mapping and analysis.

Key Features:

• Flexible barcode and adapter removal: Demultiplexes barcoded sequencing runs and removes adapter sequences from reads.
• Exact overlap sequence alignment: Uses exact overlap sequence alignment to recognize, sort, and trim sequence tags, including adapters, sample barcodes, and biological tags such as splice leader sequences.
• Multi-threaded high-performance processing: Implements SIMD and multicore parallelism for high-speed processing of large NGS datasets.
• Support for multiple data formats: Supports FASTA and FASTQ formats, including color-space reads, preserves read pairings, and can process separate barcode reads.
• Fine-grained parameter adjustment: Allows tuning of sequence tag detection parameters and search regions for customized processing.

Scientific Applications:

• Read mapping: Improves mapping rates for genome and transcriptome assemblies by removing extraneous sequence tags.
• Library demultiplexing: Sorts reads by sample barcode to enable analysis of multiplexed sequencing runs.
• Splice leader detection: Detects biological signals such as splice leader sequences (e.g., in nematodes) to support gene expression analyses.

Methodology:

Performs exact overlap sequence alignment for tag recognition and trimming, demultiplexes barcoded runs and removes adapters, employs SIMD and multicore parallelism for performance, supports FASTA/FASTQ including color-space, preserves read pairings and processes separate barcode reads, and exposes parameters to adjust detection and search regions.