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Flexbar

flexible barcode and adapter removal for sequencing platforms

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Description

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 and transcriptome assemblies. It supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform.

Several extensions were made in last months, e.g. wildcard character support for barcodes and adapters, as well as the extraction of associated read sequence characters from the alignment. In recent releases, Flexbar uses a new version of the SeqAn library and benefits in form of much higher processing speed.

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

Flexbar Web Site

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
  • Color and letter space sequencing data
  • Wildcard N for barcodes and adapters
  • Basic read filtering and trimming features
  • Trimming based on phred quality scores
  • Compressed input and output file support
  • Extensive logging features, e.g. alignments
  • Galaxy tool definition available in Tool Shed
  • Multi-threaded computation using TBB library
  • Sequence analysis based on SeqAn library

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Additional Project Details

Languages

English

Intended Audience

Science/Research

User Interface

Command-line

Programming Language

C++

Registered

2010-09-23

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