A survey of sequence alignment algorithms for next-generation sequencing

Basic local alignment search tool

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302

The Sequence Alignment/Map format and SAMtools

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041

Fast and accurate short read alignment with Burrows-Wheeler transform

Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849

Mapping and quantifying mammalian transcriptomes by RNA-Seq

Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696

Fast and accurate long-read alignment with Burrows-Wheeler transform.

Li, H., & Durbin, R. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp698 · Cited by 12,063

TopHat: discovering splice junctions with RNA-Seq

Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,682

Identification of common molecular subsequences

Smith, T. F., & Waterman, M. S. (1981) · Journal of Molecular Biology · doi:10.1016/0022-2836(81)90087-5 · Cited by 9,962

<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool

Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480

Identification of Mutations in Zebrafish Using Next‐Generation Sequencing

Henke, K., Bowen, M. E., & Harris, M. P. (2013) · Current Protocols in Molecular Biology · doi:10.1002/0471142727.mb0713s104 · Cited by 9

MEMOCODE 2012 hardware/software codesign contest: DNA sequence aligner

Edwards, S. A. (2012) · ACM/IEEE International Conference on Formal Methods and Models for Co-Design (MEMOCODE) · doi:10.1109/memcod.2012.6292303 · Cited by 9

Collinearity of protease mutations in HIV-1 samples with high-level protease inhibitor class resistance

Babrzadeh, F., Varghese, V., Pacold, M. E., Liu, T. F., Nyrén, P., Schiffer, C. A., Fessel, W. J., & Shafer, R. W. (2012) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dks409 · Cited by 9

Targeted Next-Generation Sequencing on Hirschsprung Disease: A Pilot Study Exploits DNA Pooling

Gui, H., Bao, J. Y. J., Tang, C. S.-M., So, M.-T., Ngo, D.-N., Tran, Q. A., Bui, D.-H., Pham, D.-H., Nguyen, T.-L., Tong, A. H.-Y., et al. (2014) · Annals of Human Genetics · doi:10.1111/ahg.12076 · Cited by 9

Approximate $k$ -Mer Matching Using Fuzzy Hash Maps

Healy, J., & Chambers, D. (2014) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2014.2309609 · Cited by 9

Deep sequencing approaches for the analysis of prokaryotic transcriptional boundaries and dynamics

James, K., Cockell, S., & Zenkin, N. (2017) · Methods · doi:10.1016/j.ymeth.2017.04.016 · Cited by 10

Genome Wide Approaches to Identify Protein-DNA Interactions

Ma, T., Ye, Z., & Wang, L. (2018) · Current Medicinal Chemistry · doi:10.2174/0929867325666180530115711 · Cited by 9

A Guide to Next Generation Sequence Analysis of Leishmania Genomes

Imamura, H., & Dujardin, J. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9210-2_3 · Cited by 8

Diagnostic applications of next generation sequencing: working towards quality standards/Diagnostische Anwendung von Next Generation Sequencing: Auf dem Weg zu Qualitätsstandards

Vogl, I., Eck, S. H., Benet‐Pagès, A., Greif, P. A., Hirv, K., Kotschote, S., Kuhn, M., Gehring, A., Bergmann, C., Bolz, H. J., et al. (2012) · Journal of Laboratory Medicine · doi:10.1515/labmed-2011-0032 · Cited by 9

A Survey of Multiple Sequence Alignment Techniques

Wang, X., Liu, J., Xu, Y. D., & Zhang, J. (2015) · Lecture notes in computer science · doi:10.1007/978-3-319-22180-9_52 · Cited by 9

A dynamic pipeline for RNA sequencing on multicore processors

Martínez, H., Tárraga, J., Medina, I., Barrachina, S., Castillo, M., Dopazo, J., & Quintana–Ort́ı, E. S. (2013) · European MPI Users' Group Meeting (EuroMPI) · doi:10.1145/2488551.2488581 · Cited by 9

Computational problems of analysis of short next generation sequencing reads

Boekhorst, R. T., Naumenko, F. M., Orlova, N. G., Расимовна, Г. Э., Spitsina, A. M., Витальевна, Ч. И., Orlov, Y. L., & Abnizova, I. (2016) · Vavilov Journal of Genetics and Breeding · doi:10.18699/vj16.191 · Cited by 9

smsMap: mapping single molecule sequencing reads by locating the alignment starting positions

Wei, Z., Zhang, S., & Liu, F. (2020) · BMC Bioinformatics · doi:10.1186/s12859-020-03698-w · Cited by 9

Design space exploration of dataflow-based Smith-Waterman FPGA implementations

Casale-Brunet, S., Bezati, E., & Mattavelli, M. (2017) · SiPS ... design and implementation - IEEE Workshop on Signal Processing Systems · doi:10.1109/sips.2017.8109982 · Cited by 9

Concurrent and Accurate RNA Sequencing on Multicore PlatformsPreprint

Martínez, H., Tárraga, J., Medina, I., Barrachina, S., Castillo, M., Dopazo, J., & Quintana–Ort́ı, E. S. (2013) · arXiv (Cornell University) · doi:10.48550/arxiv.1304.0681 · Cited by 9

Biclustering of High-throughput Gene Expression Data with Bicluster Miner

Király, A., Abonyi, J., Laiho, A., & Gyenesei, A. (2012) · IEEE ... International Conference on Data Mining workshops · doi:10.1109/icdmw.2012.42 · Cited by 8

Computational Epigenetics

Wei, L. K., & Au, A. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-805388-1.00012-2 · Cited by 9

Scalable genomics: From raw data to aligned reads on Apache YARN

Versaci, F., Pireddu, L., & Zanetti, G. (2016) · IEEE International Conference on Big Data (BigData) · doi:10.1109/bigdata.2016.7840727 · Cited by 8

MetaMLP: A Fast Word Embedding Based Classifier to Profile Target Gene Databases in Metagenomic Samples

Arango-Argoty, G., Heath, L. S., Pruden, A. J., Vikesland, P. J., & Zhang, L. (2021) · Journal of Computational Biology · doi:10.1089/cmb.2021.0273 · Cited by 8

2D Shapes Classification Using BLAST

Lovato, P., & Bicego, M. (2012) · Lecture notes in computer science · doi:10.1007/978-3-642-34166-3_30 · Cited by 8

Investigating Memory Optimization of Hash-index for Next Generation Sequencing on Multi-core Architecture

Wang, W., Tang, W., Li, L., Tan, G., Zhang, P., & Sun, N. (2012) · IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum · doi:10.1109/ipdpsw.2012.83 · Cited by 8

Fast and Sensitive Alignment of Microbial Whole Genome Sequencing Reads to Large Sequence Datasets on a Desktop PC: Application to Metagenomic Datasets and Pathogen Identification

Pongor, L. S., Alvarez, R. V., & Ligeti, B. (2014) · PLoS ONE · doi:10.1371/journal.pone.0103441 · Cited by 8

An optimized and low-cost FPGA-based DNA sequence alignment — A step towards personal genomics

Shah, H. A., Hasan, L., & Ahmad, N. (2013) · Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) · doi:10.1109/embc.2013.6610096 · Cited by 8

Benchmarking Short Sequence Mapping Tools

Hatem, A., Bozdağ, D., & Çatalyürek, Ü. V. (2011) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm.2011.83 · Cited by 7

HSA: A Heuristic Splice Alignment Tool

Bu, J., Chi, X., & Jin, Z. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-s2-s10 · Cited by 8

Exploring DNA Alignment-in-Memory Leveraging Emerging SOT-MRAM

Angizi, S., Zhang, W., & Fan, D. (2020) · ACM Great Lakes Symposium on VLSI (GLSVLSI) · doi:10.1145/3386263.3407590 · Cited by 8

PSimScan: Algorithm and Utility for Fast Protein Similarity Search

Kaznadzey, A., Alexandrova, N., Novichkov, V., & Kaznadzey, D. (2013) · PLoS ONE · doi:10.1371/journal.pone.0058505 · Cited by 8

Omics Informatics: From Scattered Individual Software Tools to Integrated Workflow Management Systems

Ma, T., & Zhang, A. (2016) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2016.2535251 · Cited by 10

Analysis of Genotyping-by-Sequencing (GBS) Data

Kagale, S., Koh, C., Clarke, W. E., Bollina, V., Parkin, I. A. P., & Sharpe, A. (2015) · Methods in molecular biology · doi:10.1007/978-1-4939-3167-5_15 · Cited by 8

PairMotifChIP: A Fast Algorithm for Discovery of Patterns Conserved in Large ChIP-seq Data Sets

Yu, Q., Huo, H., & Feng, D. (2016) · BioMed Research International · doi:10.1155/2016/4986707 · Cited by 8

Accelerating Pairwise Sequence Alignment Algorithm by MapReduce Technique for Next-Generation Sequencing (NGS) Data Analysis

Mondal, S., & Khatua, S. (2018) · Advances in intelligent systems and computing · doi:10.1007/978-981-13-1498-8_19 · Cited by 8

Small RNA-Seq reveals novel miRNAs shaping the transcriptomic identity of rat brain structures

Soula, A., Valere, M., López‐González, M. J., Ury‐Thiery, V., Groppi, A., Landry, M., Nikolski, M., & Favereaux, A. (2018) · Life Science Alliance · doi:10.26508/lsa.201800018 · Cited by 7

Evaluation of Whole Genome Sequencing Data

Hübschmann, D., & Schlesner, M. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9151-8_15 · Cited by 8

Genomic Evolution of Lactic Acid Bacteria

Douglas, G. L., Azcárate-Peril, M. A., & Klaenhammer, T. R. (2015) · Wiley eBooks · doi:10.1002/9781118868386.ch3 · Cited by 8

Sequence Graph Transform (SGT): A Feature Extraction Function for Sequence Data Mining.Preprint

Ranjan, C., Ebrahimi, S., & Paynabar, K. (2016) · arXiv (Cornell University) · Cited by 8

Sequence Alignment Through the Looking GlassPreprint

Appuswamy, R., Fellay, J., & Chaturvedi, N. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/256859 · Cited by 7

Kafka interfaces for composable streaming genomics pipelines

Versaci, F., Pireddu, L., & Zanetti, G. (2018) · IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI ...) · doi:10.1109/bhi.2018.8333418 · Cited by 7

Accelerating Multiple Sequence Alignments Using Parallel Computing

Baker, Q. B., Al-Hussien, R. A., & Al‐Ayyoub, M. (2024) · Computation · doi:10.3390/computation12020032 · Cited by 7

A rule-based expert system for inferring functional annotation

Xavier, D., Crespo, B., & Fuentes‐Fernández, R. (2015) · Applied Soft Computing · doi:10.1016/j.asoc.2015.05.055 · Cited by 7

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

Tran, N. H., & Chen, X. (2015) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2015.2465900 · Cited by 7

Accelerating Comparative Genomics Workflows in a Distributed Environment with Optimized Data Partitioning

Choudhury, O., Hazekamp, N., Thain, D., & Emrich, S. (2014) · IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid) · doi:10.1109/ccgrid.2014.79 · Cited by 7

Altools: a user friendly NGS data analyser

Camiolo, S., Sablok, G., & Porceddu, A. (2016) · Biology Direct · doi:10.1186/s13062-016-0110-0 · Cited by 7

Mako: A Graph-Based Pattern Growth Approach to Detect Complex Structural Variants

Lin, J., Yang, X., Kosters, W. A., Xu, T., Jia, Y., Wang, S., Zhu, Q., Ryan, M., Guo, L., Gerstein, M., et al. (2021) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2021.03.007 · Cited by 7

Guidelines and Approaches to Compliance with Regulatory and Clinical Standards: Quality Control Procedures and Quality Assurance

Lubin, I. M., Kalman, L. V., & Gargis, A. S. (2013) · Springer eBooks · doi:10.1007/978-1-4614-7001-4_14 · Cited by 7

CGAP-Align: A High Performance DNA Short Read Alignment Tool

Chen, Y., Hong, J. H., Cui, W., Zaneveld, J. E., Wang, W., Gibbs, R. A., Xiao, Y., & Chen, R. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061033 · Cited by 7

Transcriptome Analyses to Investigate the Pathogenesis of RNA Splicing Factor Retinitis Pigmentosa

Farkas, M. H., Grant, G. R., & Pierce, E. A. (2011) · Advances in experimental medicine and biology · doi:10.1007/978-1-4614-0631-0_65 · Cited by 7

DNA sequences alignment in multi-GPUs: acceleration and energy payoff

Pérez-Serrano, J., Sandes, E. F. O., de Melo, A. C. M. A., & Ujaldón, M. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2389-6 · Cited by 7

Whisper: read sorting allows robust mapping of DNA sequencing data

Deorowicz, S., Debudaj-Grabysz, A., Gudyś, A., & Grabowski, S. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty927 · Cited by 7

Gene Expression and Protein Function

Sathe, S. K., Aggarwal, S., & Tang, J. (2019) · ACM SIGKDD Explorations Newsletter · doi:10.1145/3373464.3373471 · Cited by 8

Computational Genomics

Araújo, F. A., Cavalcante, A. L. Q., Braga, M. D. B., Kato, R. B., Ramos, R. T. J., & Franco, E. F. (2021) · Springer eBooks · doi:10.1007/978-981-33-6191-1_11 · Cited by 7

SEME: A Fast Mapper of Illumina Sequencing Reads with Statistical Evaluation

Chen, S., Wang, A., & Li, L. M. (2013) · Journal of Computational Biology · doi:10.1089/cmb.2013.0111 · Cited by 7

BIM: an open ontology for the annotation of biomedical images.

Bukhari, S. A. C., Nagy, M. L., Krauthammer, M. O., Ciccarese, P., & Baker, C. J. O. (2015) · ICBO · Cited by 7

On the string matching with k mismatches

Chen, Y., & Wu, Y. (2018) · Theoretical Computer Science · doi:10.1016/j.tcs.2018.02.001 · Cited by 7

Scalable Parallel Algorithms for Genome Analysis

Georganas, E. (2016) · UC Berkeley · Cited by 7

Variant calling using NGS and sequence capture data for population and evolutionary genomic inferences in Norway Spruce ( Picea abies )Preprint

Bernhardsson, C., Wang, X., Eklöf, H., & Ingvarsson, P. K. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/805994 · Cited by 6

Screening the pathogenic causes of congenital cataract via whole exome sequencing technology in three families: Molecular genetics of congenital cataract

Qi, C., He, Y., Jiang, C. L., Zhang, X., Zhu, P., Li, W., Zhou, H., Xue, C., & Xia, X. (2023) · Molecular Medicine Reports · doi:10.3892/mmr.2023.13008 · Cited by 6

Collective effects of human genomic variation on microbiome function

New, F. N., Baer, B. R., Clark, A. G., Wells, M. T., & Brito, I. (2022) · Scientific Reports · doi:10.1038/s41598-022-07632-3 · Cited by 6

Chromatin Immunoprecipitation and High-Throughput Sequencing (ChIP-Seq): Tips and Tricks Regarding the Laboratory Protocol and Initial Downstream Data Analysis

Patten, D. K., Corleone, G., & Magnani, L. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-7774-1_15 · Cited by 6

BOCS: DNA k-mer content and scoring for rapid genetic biomarker identification at low coverage

Korshoj, L. E., & Nagpal, P. (2019) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2019.05.022 · Cited by 6

On the longest common prefix of suffixes in an inverse Lyndon factorization and other properties

Bonizzoni, P., Clelia De Felice, B., Zaccagnino, R., & Zizza, R. (2020) · Theoretical Computer Science · doi:10.1016/j.tcs.2020.10.034 · Cited by 6

Cohort analytics: efficiency and applicability

Omidvar-Tehrani, B., Amer-Yahia, S., & Lakshmanan, L. V. S. (2020) · The VLDB Journal · doi:10.1007/s00778-020-00625-6 · Cited by 6

NvWa: Enhancing Sequence Alignment Accelerator Throughput via Hardware Scheduling

Li, Y., Li, X., Gao, R., Liu, W., & Tan, G. (2023) · IEEE International Symposium on High-Performance Computer Architecture (HPCA) · doi:10.1109/hpca56546.2023.10070978 · Cited by 6

Comparing Bowtie and BWA to Align Short Reads from a RNA-Seq Experiment

Medina-Medina, N., Broka, A., Lacey, S., Lin, H., Klings, E. S., Baldwin, C. T., Steinberg, M. H., & Sebastiani, P. (2012) · Advances in Intelligent and Soft Computing · doi:10.1007/978-3-642-28839-5_23 · Cited by 6

Review of Genome Sequence Short Read Error Correction Algorithms

Tahir, M., Sardaraz, M., Ikram, A. A., & Bajwa, H. (2013) · American Journal of Bioinformatics Research · Cited by 6

Incremental DNA Sequence Analysis in the Cloud

Kienzler, R., Bruggmann, R., Ranganathan, A., & Tatbul, N. (2012) · Lecture notes in computer science · doi:10.1007/978-3-642-31235-9_50 · Cited by 6

Variant Calling Using NGS Data in European Aspen (Populus tremula)

Wang, J., Scofield, D. G., Street, N. R., & Ingvarsson, P. K. (2015) · Springer eBooks · doi:10.1007/978-3-319-17157-9_4 · Cited by 6

Understanding mapreduce-based next-generation sequencing alignment on distributed cyberinfrastructure

Mantha, P. K., Kim, N., Luckow, A., Kim, J., & Jha, S. (2012) · doi:10.1145/2483954.2483957 · Cited by 6

Sequence, a BioJS component for visualising sequences

Gómez, J., & Jiménez, R. C. (2014) · F1000Research · doi:10.12688/f1000research.3-52.v1 · Cited by 6

The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability

Li, J., Bolser, D. M., Manske, M., Giorgi, F. M., Vyahhi, N., Usadel, B., Clavijo, B., Chan, T., Wong, N., Zerbino, D. R., et al. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbt045 · Cited by 6

The Linkage Method: A Novel Approach for SNP Detection and Haplotype Reconstruction from a Single Diploid Individual Using Next-Generation Sequence Data

Sasaki, E., Sugino, R. P., & Innan, H. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst103 · Cited by 7

Profiling Short Tandem Repeats from Short Reads

Gymrek, M., & Erlich, Y. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-514-9_7 · Cited by 5

Alignment of High-Throughput Sequencing Data Inside In-Memory Databases

Daniel, F., Knaup, P., Justo, L. B., & Ganzinger, M. (2014) · Studies in health technology and informatics · doi:10.3233/978-1-61499-432-9-476 · Cited by 6

Characterization of Brassica napus L. genotypes utilizing sequence-related amplified polymorphism and genotyping by sequencing in association with cluster analysis

Lees, C. J., Li, G., & Duncan, R. W. (2016) · Molecular Breeding · doi:10.1007/s11032-016-0576-6 · Cited by 6

Next-Generation Sequencing (NGS): A Revolutionary Technology in Pharmacogenomics and Personalized Medicine

Hong, H., Zhang, W., Su, Z., Shen, J., Ge, W., Ning, B., Fang, H., Perkins, R., Shi, L. M., & Tong, W. (2013) · Springer eBooks · doi:10.1007/978-81-322-1184-6_3 · Cited by 7

Geometric ergodicity of a Metropolis-Hastings algorithm for Bayesian inference of phylogenetic branch lengths

Spade, D. A. (2020) · Computational Statistics · doi:10.1007/s00180-020-00969-1 · Cited by 6

Testing the genomic stability of the Brazilian yellow fever vaccine strain using next-generation sequencing data

de Andrade, A. A. S., Soares, A. E. R., de Almeida, L. G. P., Ciapina, L. P., Pestana, C. P., Aquino, C., Medeiros, M. A., & de Vasconcelos, A. T. R. (2021) · Interface Focus · doi:10.1098/rsfs.2020.0063 · Cited by 6

Identifying proximal RNA interactions from cDNA-encoded crosslinks with ShapeJumper

Christy, T. W., Giannetti, C. A., Laederach, A., & Weeks, K. M. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009632 · Cited by 6

Sequence Alignment Through the Looking Glass

Appuswamy, R., Fellay, J., & Chaturvedi, N. (2018) · IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum · doi:10.1109/ipdpsw.2018.00050 · Cited by 6

Dynamic Gap Selector: A Smith Waterman Sequence Alignment Algorithm with Affine Gap Model Optimisation

Urgese, G., Paciello, G., Acquaviva, A., Ficarra, E., Graziano, M., & Zamboni, M. (2014) · PORTO@Iris · Cited by 6

The Rapidly Emerging Role for Whole Exome Sequencing in Clinical Genetics

Shen, Y., Lopez, R., & Milos, P. M. (2014) · Current Genetic Medicine Reports · doi:10.1007/s40142-014-0044-8 · Cited by 6

A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data

Kakuta, M., Suzuki, S., Izawa, K., Ishida, T., & Akiyama, Y. (2017) · International Journal of Molecular Sciences · doi:10.3390/ijms18102124 · Cited by 6

Ψ-RA: a parallel sparse index for genomic read alignment

Külekci, M. O., Hon, W.-K., Shah, R., Vitter, J. S., & Xu, B. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-s2-s7 · Cited by 6

Indices and Applications in High-Throughput Sequencing

Weese, D. (2013) · Universitätsbibliothek der FU Berlin Hochschulschriftenstelle u. Dokumentenserver · doi:10.17169/refubium-11863 · Cited by 6

LISA: A Case For Learned Index based Acceleration of Biological Sequence AnalysisPreprint

Ho, D., Kalikar, S., Misra, S., Ding, J., Md, V., Tatbul, N., Li, H., & Kraska, T. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.22.423964 · Cited by 6

A Multi-Level Task Framework for Event Sequence Analysis

Zinat, K. T., Sakhamuri, S. N., Chen, A. S., & Liu, Z. (2024) · IEEE Transactions on Visualization and Computer Graphics · doi:10.1109/tvcg.2024.3456510 · Cited by 5

A Bioinformatics Approach to 3D Shape Matching

Bicego, M., Danese, S., Melzi, S., & Castellani, U. (2015) · Lecture notes in computer science · doi:10.1007/978-3-319-16220-1_22 · Cited by 5

Promoter Sequence Analysis through No Gap Multiple Sequence Alignment of Motif Pairs

Kouser, & Rangarajan, L. (2015) · Procedia Computer Science · doi:10.1016/j.procs.2015.08.031 · Cited by 5

Canonical, stable, general mapping using context schemes

Novak, A. M., Rosen, Y., Haussler, D. H., & Paten, B. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv435 · Cited by 5

Indel-tolerant read mapping with trinucleotide frequencies using cache-oblivious kd-trees

Mahmud, M. P., Wiedenhoeft, J., & Schliep, A. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts380 · Cited by 5

Leveraging known genomic variants to improve detection of variants, especially close-by Indels

Vo, N. S., & Phan, V. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty183 · Cited by 5

Diagnostic Optical Sequencing

Korshoj, L. E., & Nagpal, P. (2019) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.9b12568 · Cited by 5

On the Performance of BWA on NUMA Architectures

Lenis, J., & Senar, M. À. (2015) · IEEE International Conference on Trust, Security and Privacy in Computing and Communications (TrustCom) · doi:10.1109/trustcom.2015.638 · Cited by 5

BLESS: Bandwidth and Locality Enhanced SMEM Seeding Acceleration for DNA Sequencing

Han, S., Moon, S., Suh, T., Heo, J., & Kim, J.-Y. (2024) · Proceedings - International Symposium on Computer Architecture/Proceedings · doi:10.1109/isca59077.2024.00049 · Cited by 5

Advancing next‐generation sequencing data analytics with scalable distributed infrastructure

Kim, J., Maddineni, S., & Jha, S. (2013) · Concurrency and Computation Practice and Experience · doi:10.1002/cpe.3013 · Cited by 5

Toward Efficient Variant Calling Inside Main-Memory Database Systems

Dorok, S., Breß, S., & Saake, G. (2014) · International Workshop on Database and Expert Systems Applications (DEXA) · doi:10.1109/dexa.2014.25 · Cited by 5

Fast inexact mapping using advanced tree exploration on backward search methods

Torres, J. S., Tomás, A. E., Tárraga, J., Medina, I., Dopazo, J., & Blanquer, I. (2015) · BMC Bioinformatics · doi:10.1186/s12859-014-0438-3 · Cited by 5

STUN: querying spatio-temporal uncertain (social) networks

Kang, C., Pugliese, A., Grant, J., & Subrahmanian, V. S. (2014) · Social Network Analysis and Mining · doi:10.1007/s13278-014-0156-x · Cited by 5

In the Spotlight: Bioinformatics

Wang, M. D. (2012) · IEEE Reviews in Biomedical Engineering · doi:10.1109/rbme.2012.2228311 · Cited by 5

Concurrent and Accurate Short Read Mapping on Multicore Processors

Martinez, H., Tárraga, J., Medina, I., Barrachina, S., Castillo, M., Dopazo, J., & Quintana–Ort́ı, E. S. (2015) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2015.2392077 · Cited by 5

A survey of sequence alignment algorithms for next-generation sequencing read

Yeu, Y., Park, C., Ahn, J., Park, M., Kim, P.-G., & Park, S. (2012) · Database Research · Cited by 2

A Review on Sequence Alignment Algorithms for Short Reads Based on Next-Generation Sequencing

Kim, J., Ji, M., & Yi, G. (2020) · IEEE Access · doi:10.1109/access.2020.3031159 · Cited by 25

Sense from sequence reads: methods for alignment and assembly

Flicek, P., & Birney, E. (2009) · Nature Methods · doi:10.1038/nmeth.1376 · Cited by 357

Technology dictates algorithms: recent developments in read alignment

Alser, M., Rotman, J., Deshpande, D., Taraszka, K., Shi, H., Baykal, P. I., Yang, H. T., Xue, V., Knyazev, S., Singer, B. D., et al. (2021) · Genome Biology · doi:10.1186/s13059-021-02443-7 · Cited by 144

Comparative analysis of algorithms for next-generation sequencing read alignment

Ruffalo, M., LaFramboise, T., & Koyutürk, M. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr477 · Cited by 232