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Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading

René Rahn, Stefan Budach, Pascal Costanza, Marcel Ehrhardt, Jonny Hancox, Knut Reinert, John Hancock
2018 Bioinformatics  
topical concurrency on modern hardware using multi-threading and vectorization.  ...  With the large-scale sequence alignment we evaluate the performance of the combined acceleration using the wavefront thread-level parallelization together with the inter-sequence vectorization for a single  ... 
doi:10.1093/bioinformatics/bty380 pmid:29726911 fatcat:kydjv7smgbgh7hm6ioyuji5qpe

The SeqAn C++ template library for efficient sequence analysis: A resource for programmers

Knut Reinert, Temesgen Hailemariam Dadi, Marcel Ehrhardt, Hannes Hauswedell, Svenja Mehringer, René Rahn, Jongkyu Kim, Christopher Pockrandt, Jörg Winkler, Enrico Siragusa, Gianvito Urgese, David Weese
2017 Journal of Biotechnology  
Acknowledgements We would like to thank many people and funding agencies that supported SeqAn related projects.  ...  We also thank the anonymous reviewer who diligently pointed out small mistakes in the code examples.  ...  It is non-trivial to program efficient implementations of these components, especially if vectorization and multi-threading becomes more and more mandatory.  ... 
doi:10.1016/j.jbiotec.2017.07.017 pmid:28888961 fatcat:t4wlkxcndnbjdfzfirjh6yv624

LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment

Alberto Zeni, Giulia Guidi, Marquita Ellis, Nan Ding, Marco D. Santambrogio, Steven Hofmeyr, Aydin Buluc, Leonid Oliker, Katherine Yelick
2020 2020 IEEE International Parallel and Distributed Processing Symposium (IPDPS)  
We also demonstrate a 2.3× LOGAN speed-up versus ksw2, a state-of-art vectorized algorithm for sequence alignment implemented in minimap2, a long-read mapping software.  ...  running on two IBM Power9 processors using 168 CPU threads, with equivalent accuracy.  ...  ACKNOWLEDGMENTS We would like to thank Francesco Peverelli and Muaaz Awan for useful suggestions and valuable discussions.  ... 
doi:10.1109/ipdps47924.2020.00055 dblp:conf/ipps/ZeniGEDSHBOY20 fatcat:u7epgingcvdlbahlgn6r7bmjly

LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment [article]

Alberto Zeni, Giulia Guidi, Marquita Ellis, Nan Ding, Marco D. Santambrogio, Steven Hofmeyr, Aydın Buluç, Leonid Oliker, Katherine Yelick
2020 arXiv   pre-print
We also demonstrate a 2.3x LOGAN speed-up versus ksw2, a state-of-art vectorized algorithm for sequence alignment implemented in minimap2, a long-read mapping software.  ...  This method is particularly expensive for third-generation sequences due to the high computational cost of analyzing sequences of length between 1Kb and 1Mb.  ...  ACKNOWLEDGMENTS We would like to thank Francesco Peverelli and Muaaz Awan for useful suggestions and valuable discussions.  ... 
arXiv:2002.05200v1 fatcat:tjjmevttabh47nk4wzej4zimhe

Parallel computing for genome sequence processing

You Zou, Yuejie Zhu, Yaohang Li, Fang-Xiang Wu, Jianxin Wang
2021 Briefings in Bioinformatics  
Then, the parallel computing for genome sequence processing is discussed with four common applications: genome sequence alignment, single nucleotide polymorphism calling, genome sequence preprocessing,  ...  For each kind of application, its background is firstly introduced, and then a list of tools or algorithms are summarized in the aspects of principle, hardware platform and computing efficiency.  ...  Funding This work is supported in part by the National Natural Science Foundation of China under grants (Nos U1909208, 61732009, 61772557), Hunan Provincial Science and Technology Program (No. 2018WK4001  ... 
doi:10.1093/bib/bbab070 pmid:33822883 fatcat:a4hj2fhybrc6zlsq6xyiu6snmy

ADEPT: a domain independent sequence alignment strategy for gpu architectures

Muaaz G. Awan, Jack Deslippe, Aydin Buluc, Oguz Selvitopi, Steven Hofmeyr, Leonid Oliker, Katherine Yelick
2020 BMC Bioinformatics  
Results In this paper, we present ADEPT, a new sequence alignment strategy for GPU architectures that is domain independent, supporting alignment of sequences from both genomes and proteins.  ...  At the core of most of these tools, a significant portion of execution time is spent in determining optimal local alignment between two sequences.  ...  Acknowledgments We would like to acknowledge Francesco Peverelli, Alberto Zeni and Richard Barnes for all the sharing of knowledge and ideas.  ... 
doi:10.1186/s12859-020-03720-1 pmid:32933482 fatcat:afyd2rdpcnbw5bl3b7azppquv4

Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping

Hongyi Xin, John Greth, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu
2015 Computer applications in the biosciences : CABIOS  
Results: We present a simple and efficient algorithm, Shifted Hamming Distance (SHD), which accelerates the alignment verification procedure in read mapping, by quickly filtering out error-abundant sequence  ...  In practice, only sequence pairs with a small editdistance provide useful scientific data.  ...  Recent work has shown the potential of using single instruction multiple data (SIMD) vector execution units including general-purpose GPUs and Intel SSE Intel (2012) to accelerate local alignment techniques  ... 
doi:10.1093/bioinformatics/btu856 pmid:25577434 pmcid:PMC4426831 fatcat:vghtmhz35bcabound6logsz4zi

Fast gap-affine pairwise alignment using the wavefront algorithm

Santiago Marco-Sola, Juan Carlos Moure, Miquel Moreto, Antonio Espinosa, Peter Robinson
2020 Bioinformatics  
Results In this paper, we present the wavefront alignment algorithm (WFA), an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process  ...  As opposed to traditional dynamic programming algorithms that run in quadratic time, the WFA runs in time O(ns), proportional to the read length n and the alignment score s, using O(s2) memory.  ...  Nevertheless, the WFA can be used together with many inter-sequence paralellization techniques in order to exploit the multi-threading capabilities of modern processors.  ... 
doi:10.1093/bioinformatics/btaa777 pmid:32915952 fatcat:yiysfne44nfrbiz6di27nrm6ui

AMAS: Optimizing the Partition and Filtration of Adaptive Seeds to Speed up Read Mapping

Ngoc Hieu Tran, Xin Chen
2016 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
Keywords: next-generation sequencing, read mapping, sequence alignment, adaptive seeds, seed partition, filtration  ...  AMAS is implemented in C++ based on the SeqAn library and is freely available at https://sourceforge.net/projects/ngsamas/.  ...  Acknowledgements We thank the SeqAn team, especially the authors of Masai package for making their source codes available. Our tool uses the SeqAn library and some well-developed components of Masai.  ... 
doi:10.1109/tcbb.2015.2465900 fatcat:s6q47pnx3nfgpmzpp6kngeb4lu

Vargas: heuristic-free alignment for assessing linear and graph read aligners [article]

Charlotte A Darby, Ravi Gaddipati, Michael C Schatz, Ben Langmead
2019 bioRxiv   pre-print
While this is computationally intensive, Vargas uses multi-core parallelization and vectorized (SIMD) instructions to make it practical to optimally align large numbers of reads, achieving a maximum speed  ...  Read alignment is central to many aspects of modern genomics. Most aligners use heuristics to accelerate processing, but these heuristics can fail to find the optimal alignments of reads.  ...  We thank Daniel Baker for assistance in software development and Daehwan Kim for helpful comments on the manuscript.  ... 
doi:10.1101/2019.12.20.884676 fatcat:6tubzaio7ffhneradyksgkqx4e

Thread-cooperative, bit-parallel computation of levenshtein distance on GPU

Alejandro Chacón, Santiago Marco-Sola, Antonio Espinosa, Paolo Ribeca, Juan Carlos Moure
2014 Proceedings of the 28th ACM international conference on Supercomputing - ICS '14  
In this work we implement and optimise a CUDA version of Myers' algorithm suitable to be used as a building block for DNA sequence alignment.  ...  Our results show an overall performance of the order of tera cells updates per second using a single high-end Nvidia GPU, and factor speedups in excess of 20× with respect to a sixteen-core, non-vectorised  ...  Recent sequence alignment software tools, like BWA [10] or GEM [16] , use a two-step alignment strategy.  ... 
doi:10.1145/2597652.2597677 dblp:conf/ics/ChaconMERM14 fatcat:wo6rmx6qsjdsvlyfj56jb7dcia

Computer Architecture-Aware Optimisation of DNA Analysis Systems [article]

Hasindu Gamaarachchi
2021 arXiv   pre-print
The optimised software tools are used in complete end-to-end analysis workflows and their efficacy is demonstrated by running on prototypical embedded systems.  ...  Performing architecture-aware optimisations requires the synergistic use of knowledge from both domains, (i.e, DNA sequence analysis and computer architecture).  ...  Nanopolish is written in C/C++ and supports multi-threading through openMP.  ... 
arXiv:2101.05012v1 fatcat:wcujdqliwzgrxd2zc2wcudbqpu

DREAM-Yara: An exact read mapper for very large databases with short update time [article]

Temesgen Hailemariam Dadi, Enrico Siragusa, Vitor Piro, Andreas Andrusch, Enrico Seiler, Bernhard Renard, Knut Reinert
2018 bioRxiv   pre-print
For instance, in typical metagenomics analysis, the size of the reference sequences has become prohibitive to compute a single full- text index on standard machines.  ...  This allows us to keep the databases in several indices which can be easily rebuilt if parts are updated while maintaining a fast search time.  ...  The authors also acknowledge the support of the de.NBI network for bioinformatics infrastructure, the Intel SeqAn IPCC and the IMPRS for Scientific Computing and Computational Biology.  ... 
doi:10.1101/256354 fatcat:bvfcjgjqy5g6laguey3322c2gi

An optimized FM-index library for nucleotide and amino acid search [article]

Tim Anderson, Travis J Wheeler
2021 bioRxiv   pre-print
We present AvxWindowedFMindex (AWFM-index), an open-source, thread-parallel FM-index library written in C that is highly optimized for indexing nucleotide and amino acid sequences.  ...  , and approximately 8x faster for amino acid search in a single-threaded context.  ...  Acknowledgments 453 We thank Robert Hubley for beta testing AWFM-index and suggesting improvements to 454 the library's build process, as well as George Lesica for his help in improving the library 455  ... 
doi:10.1101/2021.01.12.426474 fatcat:4y7rqejfvzeoflvwui35vs24tm

IMSEQ—a fast and error aware approach to immunogenetic sequence analysis

Leon Kuchenbecker, Mikalai Nienen, Jochen Hecht, Avidan U. Neumann, Nina Babel, Knut Reinert, Peter N. Robinson
2015 Bioinformatics  
Availability and implementation: IMSEQ was implemented in Cþþ using the SeqAn library for efficient sequence analysis.  ...  Motivation: Recombined T-and B-cell receptor repertoires are increasingly being studied using next generation sequencing (NGS) in order to interrogate the repertoire composition as well as changes in the  ...  Funding This research was funded by the German Federal Ministry of Education and Research (BMBF) within the grants "Primage" (0315895A) to N.B. and "eKid" (01ZX1312A) to N.B. as well as by the Investitionsbank  ... 
doi:10.1093/bioinformatics/btv309 pmid:25987567 fatcat:lnequrncmrdqfhmchpf7fe4nqq
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