jtroehr edited this page Jun 14, 2018 · 39 revisions

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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. Unique molecular identifiers can be extracted in a flexible way. The program supports sequencing data in fasta and fastq format, e.g. from the Illumina platform.

Program features

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


Johannes T. Roehr, Christoph Dieterich, Knut Reinert: Flexbar 3.0 – SIMD and multicore parallelization. Bioinformatics 2017.

See article on PubMed

Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar – flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012.

See article on PubMed

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