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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
Current address: XION Medical GmbH, Pankstraße 8-10, D-13127 Berlin, Germany.
* Author to whom correspondence should be addressed.
Received: 28 August 2012; in revised form: 21 September 2012 / Accepted: 7 December 2012 / Published: 14 December 2012
Abstract: 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/.
Keywords: 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.
Dodt M, Roehr JT, Ahmed R, Dieterich C. FLEXBAR—Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms. Biology. 2012; 1(3):895-905.
Dodt, Matthias; Roehr, Johannes T.; Ahmed, Rina; Dieterich, Christoph. 2012. "FLEXBAR—Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms." Biology 1, no. 3: 895-905.