Nanopore Sequencing Technology and Tools: Computational Analysis of the Current State, Bottlenecks, and Future Directions
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[1] J. Shendure,et al. DNA sequencing at 40: past, present and future , 2017, Nature.
[2] Carlos de Lannoy,et al. A sequencer coming of age: De novo genome assembly using MinION reads. , 2017, F1000Research.
[3] C. Alkan,et al. MAGNET: Understanding and Improving the Accuracy of Genome Pre-Alignment Filtering , 2017, 1707.01631.
[4] Alberto Magi,et al. Nanopore sequencing data analysis: state of the art, applications and challenges , 2017, Briefings Bioinform..
[5] Brent S. Pedersen,et al. Nanopore sequencing and assembly of a human genome with ultra-long reads , 2017, Nature Biotechnology.
[6] S. Koren,et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation , 2016, bioRxiv.
[7] Deanna M. Church,et al. Building and Improving Reference Genome Assemblies , 2017, Proceedings of the IEEE.
[8] Niranjan Nagarajan,et al. Fast and accurate de novo genome assembly from long uncorrected reads. , 2017, Genome research.
[9] I. Birol,et al. Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art , 2016, Bioinform..
[10] Francesca Giordano,et al. Oxford Nanopore MinION Sequencing and Genome Assembly , 2016, Genom. Proteom. Bioinform..
[11] Can Alkan,et al. On genomic repeats and reproducibility , 2016, Bioinform..
[12] Niranjan Nagarajan,et al. Fast and sensitive mapping of nanopore sequencing reads with GraphMap , 2016, Nature Communications.
[13] Onur Mutlu,et al. GateKeeper: a new hardware architecture for accelerating pre‐alignment in DNA short read mapping , 2016, Bioinform..
[14] Tomáš Vinař,et al. DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads , 2016, PloS one.
[15] Matei David,et al. Nanocall: an open source basecaller for Oxford Nanopore sequencing data , 2016, bioRxiv.
[16] David A. Matthews,et al. Real-time, portable genome sequencing for Ebola surveillance , 2016, Nature.
[17] Heng Li,et al. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences , 2015, Bioinform..
[18] Vivien Marx,et al. Nanopores: a sequencer in your backpack , 2015, Nature Methods.
[19] David A. Eccles,et al. MinION Analysis and Reference Consortium: Phase 1 data release and analysis , 2015, F1000Research.
[20] Onur Mutlu,et al. Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping , 2015, Bioinform..
[21] Stefan Engelen,et al. Genome assembly using Nanopore-guided long and error-free DNA reads , 2015, BMC Genomics.
[22] T Laver,et al. Assessing the performance of the Oxford Nanopore Technologies MinION , 2015, Biomolecular detection and quantification.
[23] N. Loman,et al. A complete bacterial genome assembled de novo using only nanopore sequencing data , 2015, Nature Methods.
[24] Aaron R Quinlan,et al. Erratum: A reference bacterial genome dataset generated on the MinIONTM portable single-molecule nanopore sequencer , 2015, GigaScience.
[25] Aaron R. Quinlan,et al. A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer , 2014, bioRxiv.
[26] Quoc V. Le,et al. Sequence to Sequence Learning with Neural Networks , 2014, NIPS.
[27] C. Thermes,et al. Ten years of next-generation sequencing technology. , 2014, Trends in genetics : TIG.
[28] J. Landolin,et al. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing , 2014, Nature Biotechnology.
[29] Gabor T. Marth,et al. MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping , 2013, PloS one.
[30] Timothy P. L. Smith,et al. Reducing assembly complexity of microbial genomes with single-molecule sequencing , 2013, Genome Biology.
[31] Heng Li. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.
[32] C. Alkan,et al. Accelerating read mapping with FastHASH , 2013, BMC Genomics.
[33] Nuno A. Fonseca,et al. Tools for mapping high-throughput sequencing data , 2012, Bioinform..
[34] Knut Reinert,et al. Fast and accurate read mapping with approximate seeds and multiple backtracking , 2012, Nucleic acids research.
[35] Carl Ebeling,et al. Hardware Acceleration of Short Read Mapping , 2012, 2012 IEEE 20th International Symposium on Field-Programmable Custom Computing Machines.
[36] S. Salzberg,et al. Repetitive DNA and next-generation sequencing: computational challenges and solutions , 2011, Nature Reviews Genetics.
[37] Ümit V. Çatalyürek,et al. Benchmarking short sequence mapping tools , 2013, BMC Bioinformatics.
[38] Pavel A Pevzner,et al. How to apply de Bruijn graphs to genome assembly. , 2011, Nature biotechnology.
[39] Lucian Ilie,et al. SHRiMP2: Sensitive yet Practical Short Read Mapping , 2011, Bioinform..
[40] Faraz Hach,et al. mrsFAST: a cache-oblivious algorithm for short-read mapping , 2010, Nature Methods.
[41] Richard Durbin,et al. Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..
[42] Peter M. Rice,et al. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants , 2009, Nucleic acids research.
[43] K. Reinert,et al. RazerS--fast read mapping with sensitivity control. , 2009, Genome research.
[44] J. Kitzman,et al. Personalized Copy-Number and Segmental Duplication Maps using Next-Generation Sequencing , 2009, Nature Genetics.
[45] Mihai Pop,et al. Genome assembly reborn: recent computational challenges , 2009, Briefings Bioinform..
[46] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[47] Michael Brudno,et al. SHRiMP: Accurate Mapping of Short Color-space Reads , 2009, PLoS Comput. Biol..
[48] Michael C. Schatz,et al. CloudBurst: highly sensitive read mapping with MapReduce , 2009, Bioinform..
[49] H. Bayley,et al. Continuous base identification for single-molecule nanopore DNA sequencing. , 2009, Nature nanotechnology.
[50] Cole Trapnell,et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.
[51]
R. Durbin,et al.
Mapping Quality Scores Mapping Short Dna Sequencing Reads and Calling Variants Using P ,
2022
.
[52]
D. Branton,et al.
The potential and challenges of nanopore sequencing
,
2008,
Nature Biotechnology.
[53]
Dean M. Tullsen,et al.
Initial observations of the simultaneous multithreading Pentium 4 processor
,
2003,
2003 12th International Conference on Parallel Architectures and Compilation Techniques.
[54]
David A. Koufaty,et al.
Hyperthreading Technology in the Netburst Microarchitecture
,
2003,
IEEE Micro.
[55]
Christopher J. Lee,et al.
Multiple sequence alignment using partial order graphs
,
2002,
Bioinform..
[56]
P. Pevzner,et al.
An Eulerian path approach to DNA fragment assembly
,
2001,
Proceedings of the National Academy of Sciences of the United States of America.
[57]
Juha Kärkkäinen,et al.
Better Filtering with Gapped q-Grams
,
2001,
Fundam. Informaticae.
[58]
Kuldip K. Paliwal,et al.
Bidirectional recurrent neural networks
,
1997,
IEEE Trans. Signal Process..
[59]
Dean M. Tullsen,et al.
Simultaneous multithreading: a platform for next-generation processors
,
1997,
IEEE Micro.
[60]
D. Branton,et al.
Characterization of individual polynucleotide molecules using a membrane channel.
,
1996,
Proceedings of the National Academy of Sciences of the United States of America.
[61]
S. Eddy.
Hidden Markov models.
,
1996,
Current opinion in structural biology.
[62]
Jack L. Lo,et al.
Exploiting Choice: Instruction Fetch and Issue on an Implementable Simultaneous Multithreading Processor
,
1996,
23rd Annual International Symposium on Computer Architecture (ISCA'96).
[63]
Mario Nemirovsky,et al.
Increasing superscalar performance through multistreaming
,
1995,
PACT.
[64]
Dean M. Tullsen,et al.
Simultaneous multithreading: Maximizing on-chip parallelism
,
1995,
Proceedings 22nd Annual International Symposium on Computer Architecture.
[65]
Kozo Kimura,et al.
An Elementary Processor Architecture with Simultaneous Instruction Issuing from Multiple Threads
,
1992,
[1992] Proceedings the 19th Annual International Symposium on Computer Architecture.
[66]
Barak A. Pearlmutter.
Learning State Space Trajectories in Recurrent Neural Networks
,
1989,
Neural Computation.
[67]
D. Lipman,et al.
Improved tools for biological sequence comparison.
,
1988,
Proceedings of the National Academy of Sciences of the United States of America.
[68]
Jr. G. Forney,et al.
Viterbi Algorithm
,
1973,
Encyclopedia of Machine Learning.
[69]
Nan Li,et al.
Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph.
,
2012,
Briefings in functional genomics.
[70]
E. Eichler,et al.
Limitations of next-generation genome sequence assembly
,
2011,
Nature Methods.
[71]
William Magro,et al.
Hyper-Threading Technology: Impact on Compute-Intensive Workloads
,
2002
.