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Biology 2012, 1(3), 895-905; doi:10.3390/biology1030895
Article

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

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Received: 28 August 2012; in revised form: 21 September 2012 / Accepted: 7 December 2012 / Published: 14 December 2012
(This article belongs to the Special Issue Next Generation Sequencing Approaches in Biology)
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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 high-throughput sequencing; demultiplexing; trimming; clipping; quality control
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

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.

AMA Style

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.

Chicago/Turabian Style

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.



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