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References from From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures. Local targets link to admitted publications; unresolved targets remain external evidence.
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2016 · External reference
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SneakySnake: A fast and accurate universal genome pre-alignment filter for CPUs, GPUs, and FPGAs
2020 · External reference
GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies
10.1186/s12864-018-4460-0 · 2018 · External reference
10.1145/3503222.3507702
10.1145/3503222.3507702 · 2022 · External reference
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10.1109/mm.2021.3088396 · 2021 · External reference
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10.1073/pnas.74.12.5463
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10.1101/2021.02.05.429867 · 2021 · External reference
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2009 · External reference
10.1016/j.yexcr.2014.01.008
10.1016/j.yexcr.2014.01.008 · External reference
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10.1186/gb-2010-11-11-r116 · 2010 · External reference
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10.1186/s13059-018-1554-6
10.1186/s13059-018-1554-6 · External reference
10.1038/nrg.2016.57
10.1038/nrg.2016.57 · External reference
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10.1093/bioinformatics/btaa835 · External reference
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10.1093/gigascience/gix010 · 2017 · External reference
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10.1101/2022.01.31.478527
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10.1093/bioinformatics/btr708
10.1093/bioinformatics/btr708 · External reference
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10.1186/s13059-021-02265-7 · 2021 · External reference
PBSIM: PacBio reads simulator—toward accurate genome assembly
10.1093/bioinformatics/bts649 · 2012 · External reference
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10.1016/j.tig.2014.07.001
10.1016/j.tig.2014.07.001 · External reference
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10.1111/j.1755-0998.2011.03024.x
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10.1038/s41587-021-01108-x
10.1038/s41587-021-01108-x · External reference
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10.1186/s13059-021-02282-6 · 2021 · External reference
10.1186/s13059-020-1935-5
10.1186/s13059-020-1935-5 · External reference
Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm
10.1093/bioinformatics/btaa179 · 2020 · External reference
10.1038/s41576-020-0236-x
10.1038/s41576-020-0236-x · External reference
Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions
10.1093/bib/bby017 · 2019 · External reference
Advent of a new sequencing era: long-read and on-site sequencing
10.1038/s10038-019-0683-4 · 2020 · External reference
Highly accurate long-read HiFi sequencing data for five complex genomes
10.1038/s41597-020-00743-4 · 2020 · External reference
10.1038/s41587-019-0217-9
10.1038/s41587-019-0217-9 · External reference
10.1038/nrg3933
10.1038/nrg3933 · External reference
10.1038/nbt.4060
10.1038/nbt.4060 · External reference
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2019 · External reference
10.1038/s41467-018-07271-1
10.1038/s41467-018-07271-1 · External reference
10.1101/gr.215087.116
10.1101/gr.215087.116 · External reference
Efficient assembly of nanopore reads via highly accurate and intact error correction
2021 · External reference
Finding the right fit: evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data
2022 · External reference
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A Comparison of base-calling algorithms for illumina sequencing technology
10.1093/bib/bbv088 · 2016 · External reference
HiLive – real-time mapping of illumina reads while sequencing
2016 · External reference
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10.1186/s13059-018-1462-9
10.1186/s13059-018-1462-9 · External reference
10.1186/s13059-019-1727-y
10.1186/s13059-019-1727-y · External reference
10.1145/3410463.3414626
10.1145/3410463.3414626 · 2020 · External reference
10.1109/micro56248.2022.00067
10.1109/micro56248.2022.00067 · External reference
10.1145/3445814.3446749
10.1145/3445814.3446749 · 2021 · External reference
10.1109/iccd50377.2020.00035
10.1109/iccd50377.2020.00035 · 2020 · External reference
A scalable near-memory architecture for training deep neural networks on large in-memory datasets
10.1109/tc.2018.2876312 · 2019 · External reference
Fast-bonito: A faster deep learning based basecaller for nanopore sequencing
10.1016/j.ailsci.2021.100011 · 2021 · External reference
Beyond sequencing: machine learning algorithms extract biology hidden in Nanopore signal data
10.1016/j.tig.2021.09.001 · 2022 · External reference
GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis
10.1186/s12859-020-03697-x · 2020 · External reference
Real-time selective sequencing using nanopore technology
10.1038/nmeth.3930 · 2016 · External reference
Unresolved reference
2021 · External reference
10.1038/s41587-020-0731-9
10.1038/s41587-020-0731-9 · External reference
Real-time mapping of nanopore raw signals
10.1093/bioinformatics/btab264 · 2021 · External reference
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10.1093/bioinformatics/bty191
10.1093/bioinformatics/bty191 · External reference
Edlib: a C/C++ library for fast, exact sequence alignment using edit distance
10.1093/bioinformatics/btw753 · 2017 · External reference
Quality control of next-generation sequencing data without a reference
10.3389/fgene.2014.00111 · 2014 · External reference
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2020 · External reference
10.1080/10635150500354886
10.1080/10635150500354886 · External reference
10.1002/anie.201105717
10.1002/anie.201105717 · External reference
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LongQC, a quality control tool for third generation sequencing long
2020 · External reference
RabbitQC: high-speed scalable quality control for sequencing data
10.1093/bioinformatics/btaa719 · 2021 · External reference
10.1093/bioinformatics/btz234
10.1093/bioinformatics/btz234 · External reference
10.1093/bioinformatics/btp352
10.1093/bioinformatics/btp352 · External reference
10.1145/2746539.2746612
10.1145/2746539.2746612 · External reference
10.1093/bioinformatics/btv670
10.1093/bioinformatics/btv670 · External reference
10.1101/2022.11.23.517691
10.1101/2022.11.23.517691 · External reference
10.1145/872757.872770
10.1145/872757.872770 · External reference
10.1093/bioinformatics/btaa435
10.1093/bioinformatics/btaa435 · External reference
Accelerating read mapping with FastHASH
10.1186/1471-2164-14-s1-s13 · 2013 · External reference
Syncmers are more sensitive than minimizers for selecting conserved k-mers in biological sequences
10.7717/peerj.10805 · 2021 · External reference
10.1371/journal.pcbi.1010638
10.1371/journal.pcbi.1010638 · External reference
PatternHunter: faster and more sensitive homology search
10.1093/bioinformatics/18.3.440 · 2002 · External reference
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10.1101/gr.275648.121 · 2021 · External reference
Efficient computation of spaced seed hashing with block indexing
10.1186/s12859-018-2415-8 · 2018 · External reference
S-conLSH: alignment-free gapped mapping of noisy long reads
10.1186/s12859-020-03918-3 · 2021 · External reference
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10.1038/nbt.3238
10.1038/nbt.3238 · External reference
10.1093/bioinformatics/btw152
10.1093/bioinformatics/btw152 · External reference
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10.1109/ipdps.2019.00041
10.1109/ipdps.2019.00041 · External reference
An optimized FM-index library for nucleotide and amino acid search
10.1186/s13015-021-00204-6 · 2021 · External reference
10.1109/isca52012.2021.00038
10.1109/isca52012.2021.00038 · 2021 · External reference
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10.1038/s43588-022-00201-8 · 2022 · External reference
10.1145/3352460.3358329
10.1145/3352460.3358329 · External reference
10.1109/dac.2018.8465882
10.1109/dac.2018.8465882 · External reference
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10.1093/bioinformatics/btx342
10.1093/bioinformatics/btx342 · External reference
10.1093/bioinformatics/btu856
10.1093/bioinformatics/btu856 · External reference
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10.1145/3352460.3358308
10.1145/3352460.3358308 · 2019 · External reference
GASSST: global alignment short sequence search tool
10.1093/bioinformatics/btq485 · 2010 · External reference
10.1109/access.2022.3153032
10.1109/access.2022.3153032 · External reference
mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications
10.1093/nar/gku370 · 2014 · External reference
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2021 · External reference
RazerS 3: faster, fully sensitive read mapping
10.1093/bioinformatics/bts505 · 2012 · External reference
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10.1093/bioinformatics/btv662
10.1093/bioinformatics/btv662 · External reference
10.1109/fccm.2019.00027
10.1109/fccm.2019.00027 · 2019 · External reference
10.1101/2022.03.09.483575
10.1101/2022.03.09.483575 · External reference
Accurate high throughput alignment via line sweep-based seed processing
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10.1016/0022-2836(82)90398-9 · External reference
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10.1016/0022-0000(80)90002-1 · 1980 · External reference
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10.1016/s0019-9958(85)80046-2 · 1985 · External reference
Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments
10.1186/s12859-016-0930-z · 2016 · External reference
Fast gap-affine pairwise alignment using the wavefront algorithm
10.1093/bioinformatics/btaa777 · 2021 · External reference
10.1101/2022.01.12.476087
10.1101/2022.01.12.476087 · External reference
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A Generalization of the Landau-Vishkin Algorithm with Custom Gap Penalties
2017 · External reference
GASAL2: a GPU accelerated sequence alignment library for high-throughput NGS data
10.1186/s12859-019-3086-9 · 2019 · External reference
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10.1101/2022.04.18.488374
10.1101/2022.04.18.488374 · External reference
FPGASW: Accelerating large-scale smith–Waterman sequence alignment application with backtracking on FPGA linear systolic array
10.1007/s12539-017-0225-8 · 2018 · External reference
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10.1109/mc.1982.1653825 · 1982 · External reference
10.1109/micro50266.2020.00080
10.1109/micro50266.2020.00080 · 2020 · External reference
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10.1109/isca.2018.00017
10.1109/isca.2018.00017 · 2018 · External reference
10.1109/islped.2019.8824830
10.1109/islped.2019.8824830 · External reference
CUDAlign 4.0: incremental speculative traceback for exact chromosome-wide alignment in GPU clusters
10.1109/tpds.2016.2515597 · 2016 · External reference
10.1109/ipdpsw55747.2022.00039
10.1109/ipdpsw55747.2022.00039 · External reference
Accelerating the next generation long read mapping with the FPGA-based system
10.1109/tcbb.2014.2326876 · 2014 · External reference
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10.1145/316542.316550 · 1999 · External reference
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10.1093/bioinformatics/btu507 · 2014 · External reference
10.1109/tc.2018.2875733
10.1109/tc.2018.2875733 · External reference
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10.1145/1109557.1109644
10.1145/1109557.1109644 · External reference
Approximating edit distance in near-linear time
10.1137/090767182 · 2012 · External reference
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2018 · External reference
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10.1186/1471-2105-6-31 · 2005 · External reference
10.1089/10665270050081478
10.1089/10665270050081478 · External reference
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2020 · External reference
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10.1101/2021.11.08.467651 · External reference
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10.1038/nbt.4235
10.1038/nbt.4235 · External reference
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10.1186/s13073-020-00791-w · External reference
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10.1038/s41587-020-0538-8 · External reference
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10.1186/s12864-020-6455-x · 2020 · External reference
A comprehensive benchmarking of WGS-based deletion structural variant callers
10.1093/bib/bbac221 · 2022 · External reference
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Scaling accurate genetic variant discovery to tens of thousands of samples
2018 · External reference
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10.1186/s13059-022-02636-8
10.1186/s13059-022-02636-8 · External reference
DeepSV: accurate calling of genomic deletions from high-throughput sequencing data using deep convolutional neural network
10.1186/s12859-019-3299-y · 2019 · External reference
Detection of chromosome structural variation by targeted next-generation sequencing and a deep learning application
10.1038/s41598-019-40364-5 · 2019 · External reference
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2018 · External reference
10.1101/115717
10.1101/115717 · External reference
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10.1371/journal.pone.0132868 · 2015 · External reference
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10.1371/journal.pone.0244471 · 2021 · External reference
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10.1145/3400286.3418243 · External reference
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10.7717/peerj.421 · 2014 · External reference
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Ultra-fast next generation human genome sequencing data processing using DRAGENTM bio-IT processor for precision medicine
10.4236/ojgen.2017.71002 · 2017 · External reference
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10.1038/s41588-018-0273-y · External reference
Is it time to change the reference genome?
10.1186/s13059-019-1774-4 · 2019 · External reference
Genome graphs and the evolution of genome inference
10.1101/gr.214155.116 · 2017 · External reference
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10.1093/bioinformatics/btac554
10.1093/bioinformatics/btac554 · External reference
Fast nanopore sequencing data analysis with SLOW5
10.1038/s41587-021-01147-4 · 2022 · External reference
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10.1093/bioinformatics/btac528 · 2022 · External reference