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flexible barcode and adapter removal for sequencing platforms

5.0 Stars (9)
8 Downloads (This Week)
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Flexbar moved to https://github.com/seqan/flexbar

The program Flexbar processes high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar supports next-generation sequencing data in fasta and fastq format, e.g. from the Illumina platform.

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.

Flexbar Web Site


  • Demultiplexing of barcoded sequencing runs
  • Detection and removal of adapter sequences
  • Paired reads and separate barcode reads
  • Sequence analysis based on SeqAn library


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User Ratings

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

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

    does what it says. fast

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

    Output files are truncated when processing sanger-fastq using this command-line: flexbar -n 32 -t flexbar-3 -f fastq-sanger -s 121025_0005_000000000-A2056_1.sanfastq -a linker3.fasta -ae RIGHT -at 1 -aa -m 15 >flexbar-3.fastq.log 2>&1 I've not looked at the sources, but it might be a failure to flush the ouput stream.

    Posted 02/12/2013
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