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Flexbar — flexible barcode and adapter removal

The program Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar increases read mapping rates and improves genome as well as transcriptome assemblies. It supports next-generation sequencing data in fasta and fastq format from Illumina and the Roche 454 platform.

• Flexbar manual
• Program options
• Setup instructions
• Contact jtroehr for support
• View other SeqAn repositories

Program features

• Demultiplexing of barcoded sequencing runs
• Detection and removal of adapter sequences
• Exact global alignment with free end-gaps
• Paired reads and separate barcode reads
• Wildcard N for barcodes and adapters
• Basic read filtering and trimming features
• Compressed input and output file support
• Extensive logging features, e.g. alignments
• Galaxy tool definition available in Tool Shed
• Multithreaded computation based on TBB library
• Sequence analysis based on SeqAn library

Reference

Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar — flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012, 1(3):895-905.

See article on PubMed.