Knut Reinert1, Temesgen Hailemariam Dadi2, Marcel Ehrhardt2, Hannes Hauswedell2, Svenja Mehringer2, René Rahn2, Jongkyu Kim3, Christopher Pockrandt3, Jörg Winkler3, Enrico Siragusa4, Gianvito Urgese5, David Weese6. 1. Algorithmic Bioinformatics, Institute for Bioinformatics, FU Berlin, Takustrasse 9, 14195 Berlin, Germany. Electronic address: knut.reinert@fu-berlin.de. 2. Algorithmic Bioinformatics, Institute for Bioinformatics, FU Berlin, Takustrasse 9, 14195 Berlin, Germany. 3. Efficient Algorithms for -Omics Data, Max Planck Institute for Molecular Genetics, Ihnestrasse 62-73, 14195 Berlin, Germany. 4. IBM Watson Research, Yorktown Heights, NY, USA. 5. Department of Control and Computer Engineering, Politecnico di Torino, Italy. 6. SAP Innovation Center, Potsdam, Germany.
Abstract
BACKGROUND: The use of novel algorithmic techniques is pivotal to many important problems in life science. For example the sequencing of the human genome (Venter et al., 2001) would not have been possible without advanced assembly algorithms and the development of practical BWT based read mappers have been instrumental for NGS analysis. However, owing to the high speed of technological progress and the urgent need for bioinformatics tools, there was a widening gap between state-of-the-art algorithmic techniques and the actual algorithmic components of tools that are in widespread use. We previously addressed this by introducing the SeqAn library of efficient data types and algorithms in 2008 (Döring et al., 2008). RESULTS: The SeqAn library has matured considerably since its first publication 9 years ago. In this article we review its status as an established resource for programmers in the field of sequence analysis and its contributions to many analysis tools. CONCLUSIONS: We anticipate that SeqAn will continue to be a valuable resource, especially since it started to actively support various hardware acceleration techniques in a systematic manner.
BACKGROUND: The use of novel algorithmic techniques is pivotal to many important problems in life science. For example the sequencing of the human genome (Venter et al., 2001) would not have been possible without advanced assembly algorithms and the development of practical BWT based read mappers have been instrumental for NGS analysis. However, owing to the high speed of technological progress and the urgent need for bioinformatics tools, there was a widening gap between state-of-the-art algorithmic techniques and the actual algorithmic components of tools that are in widespread use. We previously addressed this by introducing the SeqAn library of efficient data types and algorithms in 2008 (Döring et al., 2008). RESULTS: The SeqAn library has matured considerably since its first publication 9 years ago. In this article we review its status as an established resource for programmers in the field of sequence analysis and its contributions to many analysis tools. CONCLUSIONS: We anticipate that SeqAn will continue to be a valuable resource, especially since it started to actively support various hardware acceleration techniques in a systematic manner.
Authors: Thomas Desvignes; Phillipe Loher; Karen Eilbeck; Jeffery Ma; Gianvito Urgese; Bastian Fromm; Jason Sydes; Ernesto Aparicio-Puerta; Victor Barrera; Roderic Espín; Florian Thibord; Xavier Bofill-De Ros; Eric Londin; Aristeidis G Telonis; Elisa Ficarra; Marc R Friedländer; John H Postlethwait; Isidore Rigoutsos; Michael Hackenberg; Ioannis S Vlachos; Marc K Halushka; Lorena Pantano Journal: Bioinformatics Date: 2020-02-01 Impact factor: 6.937
Authors: Pay Giesselmann; Björn Brändl; Etienne Raimondeau; Rebecca Bowen; Christian Rohrandt; Rashmi Tandon; Helene Kretzmer; Günter Assum; Christina Galonska; Reiner Siebert; Ole Ammerpohl; Andrew Heron; Susanne A Schneider; Julia Ladewig; Philipp Koch; Bernhard M Schuldt; James E Graham; Alexander Meissner; Franz-Josef Müller Journal: Nat Biotechnol Date: 2019-11-18 Impact factor: 54.908