Next Article in Journal
Climate Change Impacts on the Tree of Life: Changes in Phylogenetic Diversity Illustrated for Acropora Corals
Next Article in Special Issue
Next-Generation Sequencing: From Understanding Biology to Personalized Medicine
Previous Article in Journal
Climate Predictions Accelerate Decline for Threatened Macrozamia Cycads from Queensland, Australia
Previous Article in Special Issue
Whole Genome Sequencing and a New Bioinformatics Platform Allow for Rapid Gene Identification in D. melanogaster EMS Screens
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
Author to whom correspondence should be addressed.
Current address: XION Medical GmbH, Pankstraße 8-10, D-13127 Berlin, Germany.
Biology 2012, 1(3), 895-905;
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: View Full-Text
Keywords: high-throughput sequencing; demultiplexing; trimming; clipping; quality control high-throughput sequencing; demultiplexing; trimming; clipping; quality control
Show Figures

Figure 1

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.

Show more citation formats Show less citations formats

Article Access Map by Country/Region

Only visits after 24 November 2015 are recorded.
Search more from Scilit
Back to TopTop