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Flexbar

flexible barcode and adapter removal for sequencing platforms

5.0 Stars (9)
26 Downloads (This Week)
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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.

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
  • 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
  • Multi-threaded computation of alignments
  • Sequence analysis based on SeqAn library

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ease 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 0 / 5
features 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 0 / 5
design 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 0 / 5
support 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 0 / 5
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User Reviews

  • ashleydean
    1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    Thanks for Flexbar, it's perfect!

    Posted 06/09/2013
  • anon-4b7155ac86502b2d55001197
    1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    does what it says. fast

    Posted 02/13/2013
  • cybermat
    1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    Hi aue0618! Yes you are right - there was a bug introduced that got fixed in the latest version! Thanks for the hint- just download 2.13 and it should work again!

    Posted 02/13/2013
  • josephmitchell
    1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    theflexibleadap works perfectly.

    Posted 02/12/2013
  • oid-3803663
    1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    I like your program, but the reporting of the stats is a little confusing for Pair end data. It is not easy to understand how many PAIRS you have removed based on it not passing one of the filters. If one of the pairs contains an N, you report 1 read (of two total) containing an N, but you also remove the other reads (as you should) but you don't report this number. So if BOTH reads contained the N, you ALSO report 1 for the Discard N but still only remove 1 read pair....Even though there are 2 reads with an N Also, it seems that the USED field is always the same as the READS IN FILE field...I would have expected the USED field to be READS IN FILE minus DISCARD_B minus DISCARD_QUAL Or am I missing something ?

    Posted 02/12/2013
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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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