Repository: Freie Universität Berlin, Math Department

Flexbar 3.0 – SIMD and multicore parallelization

Roehr, Johannes T. and Dieterich, Christoph and Reinert, Knut (2017) Flexbar 3.0 – SIMD and multicore parallelization. Bioinformatics, 33 (18). pp. 2941-2942. ISSN 1367-4803

Full text not available from this repository.

Official URL:


Motivation: High-throughput sequencing machines can process many samples in a single run. For Illumina systems, sequencing reads are barcoded with an additional DNA tag that is contained in the respective sequencing adapters. The recognition of barcode and adapter sequences is hence commonly needed for the analysis of next-generation sequencing data. Flexbar performs demultiplexing based on barcodes and adapter trimming for such data. The massive amounts of data generated on modern sequencing machines demand that this preprocessing is done as efficiently as possible. Results: We present Flexbar 3.0, the successor of the popular program Flexbar. It employs now twofold parallelism: multi-threading and additionally SIMD vectorization. Both types of parallelism are used to speed-up the computation of pair-wise sequence alignments, which are used for the detection of barcodes and adapters. Furthermore, new features were included to cover a wide range of applications. We evaluated the performance of Flexbar based on a simulated sequencing dataset. Our program outcompetes other tools in terms of speed and is among the best tools in the presented quality benchmark. Availability and implementation: Contact: or

Item Type:Article
Subjects:Mathematical and Computer Sciences > Computer Science
Divisions:Department of Mathematics and Computer Science > Institute of Computer Science > Algorithmic Bioinformatics Group
ID Code:2117
Deposited By: Anja Kasseckert
Deposited On:12 Oct 2017 12:16
Last Modified:12 Oct 2017 12:16

Repository Staff Only: item control page