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Open AccessArticle

FLEXBAR—Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms

Bioinformatics in Quantitative Biology, Berlin Institute for Medical Systems Biology at the Max Delbrück Centre for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
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Current address: XION Medical GmbH, Pankstraße 8-10, D-13127 Berlin, Germany.
Biology 2012, 1(3), 895-905; https://doi.org/10.3390/biology1030895
Received: 28 August 2012 / Revised: 21 September 2012 / Accepted: 7 December 2012 / Published: 14 December 2012
(This article belongs to the Special Issue Next Generation Sequencing Approaches in Biology)
Quantitative and systems biology approaches benefit from the unprecedented depth of next-generation sequencing. A typical experiment yields millions of short reads, which oftentimes carry particular sequence tags. These tags may be: (a) specific to the sequencing platform and library construction method (e.g., adapter sequences); (b) have been introduced by experimental design (e.g., sample barcodes); or (c) constitute some biological signal (e.g., splice leader sequences in nematodes). Our software FLEXBAR enables accurate recognition, sorting and trimming of sequence tags with maximal flexibility, based on exact overlap sequence alignment. The software supports data formats from all current sequencing platforms, including color-space reads. FLEXBAR maintains read pairings and processes separate barcode reads on demand. Our software facilitates the fine-grained adjustment of sequence tag detection parameters and search regions. FLEXBAR is a multi-threaded software and combines speed with precision. Even complex read processing scenarios might be executed with a single command line call. We demonstrate the utility of the software in terms of read mapping applications, library demultiplexing and splice leader detection. FLEXBAR and additional information is available for academic use from the website: http://sourceforge.net/projects/flexbar/. View Full-Text
Keywords: high-throughput sequencing; demultiplexing; trimming; clipping; quality control high-throughput sequencing; demultiplexing; trimming; clipping; quality control
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Dodt, M.; Roehr, J.T.; Ahmed, R.; Dieterich, C. FLEXBAR—Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms. Biology 2012, 1, 895-905.

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