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Real-time mapping of nanopore raw signals

Haowen Zhang, Haoran Li, Chirag Jain, Haoyu Cheng, Kin Fai Au, Heng Li, Srinivas Aluru
<span title="2021-07-01">2021</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Results In this work, we present a new streaming method that can map nanopore raw signals for real-time selective sequencing.  ...  Then we evaluated it on both simulated and real data and compared it to the state-of-the-art nanopore raw signal mapper Uncalled.  ...  Second, we plan to study whether Sigmap can be adapted to map RNA nanopore raw signals.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btab264">doi:10.1093/bioinformatics/btab264</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34252938">pmid:34252938</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/i2ypqxrbwfhxzeuoxgcpovemtu">fatcat:i2ypqxrbwfhxzeuoxgcpovemtu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210714170254/https://watermark.silverchair.com/btab264.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAvQwggLwBgkqhkiG9w0BBwagggLhMIIC3QIBADCCAtYGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMnn0IMByueTYCpX6bAgEQgIICp6P-gQFCEb9MYRvOPdMTdyw_FldCVyTeznbkLbncqNrYMX-kV3Q1-VmNd5wrMTOldj7JMn_UHludQezPuk0hLg_xyV5NRAVxK6FM5JOFLjIU2ixmzUs-COyOJd1EiJcvEpm7cuH-axtoXFwLDyEsdAN8WBHnqF3zjpiN5PpxF1jd_lOFKpkVQKrOfg-6FN-b6NW3ikOZrYp06D-ZYmJ70mh9OLEW8gAFu2Jl3zqzxCP85cWjtotlLBFgKWlnwxNrAI1AcZ0LOILPMcp6GjuwU9fQdkpPo_VmR9-hOdqg4NDMR7KNyL05T79D8k3Op96Gj4HcuIYbAoAhmBikCm23aNNjspAPwggV4hwTmktLwqoDHlEHXurvKsv-xUJ_U45UFTytl2_qNhv8XW7so6gJq-0IEV-OPGIlarvrwvk7O1S3ESnn8pWqfRn2OdonZIfcgyoLun0TdC0ukcgKF5nAe845o0SL8osovWtxhgtQp5DTVXBEmqHEJs8JP6gUYlTRhu92Gvf-9-CzwhdEZgWiIf3f3ZS5OmdLrviNU5T5E76BpmD8pIxybMzmVRiHhFMdduS7GxTAKpQItCtZJ5bSRLk7F7yelYoQRV8bSlxWwYCK9UyP1ODclIyK2z5Cn_dG_7HyavP_Ls7AVrGx43jMMgYHxdgAAlMaNHG_Xe5GTl6W_EtFP6crk4T25ONzuFKEEDNxLGCE3NamghyqNYTHUfqhmETE-6k1m17fXjM_Kdwf9nN6QNhlGLBsh7xE7Mjiihn_fb3cpRXtz7HvIkWfhfb8k67AJ_h-e3z5S3yir1uESNCCTD6pk8fY8FCfy0z1ALo55WKTdv3BchBYQcvfbwDhYUw8afbg-Qc6I6Z-51dq4Nr7Y2aod58xyaHYtY-upm26mfMJ8PU" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c6/e5/c6e5fc1944dcb872b7afa0eba9ae03bc22756f06.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btab264"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a>

Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED [article]

Sam Kovaka, Yunfan Fan, Bohan Ni, Winston Timp, Michael C Schatz
<span title="2020-02-03">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
ReadUntil sequencing allows nanopore devices to selectively eject individual reads from the pore in real-time.  ...  Here we present UNCALLED (github.com/skovaka/UNCALLED), an open-source mapper that rapidly matches streaming nanopore current signals to a reference sequence.  ...  This work was funded, in part, by the US National Science Foundation (NSF) grant DBI-1350041 (MCS) and US National Institute of Health (NIH) grant 1R01HG009190 (WT). WT holds two patents  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.02.03.931923">doi:10.1101/2020.02.03.931923</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vl547t3mffaqbmvzki2ig4vr7e">fatcat:vl547t3mffaqbmvzki2ig4vr7e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200326070945/https://www.biorxiv.org/content/biorxiv/early/2020/02/03/2020.02.03.931923.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c7/da/c7daf6b4938f69781c3d909ca9bab8fe307e0a4e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.02.03.931923"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Novel algorithms for efficient subsequence searching and mapping in nanopore raw signals towards targeted sequencing [article]

Renmin Han, Sheng Wang, Xin Gao
<span title="2018-12-09">2018</span> <i title="Cold Spring Harbor Laboratory"> biorxiv/medrxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
and accurately search and map genomic subsequences of interest in a pool of nanopore reads (or raw signals).  ...  Comprehensive experiments on real-world nanopore datasets show the efficiency and effectiveness of the proposed algorithms.  ...  Coin, Louise Roddam and Tania Duarte for providing the nanopore sequencing data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/491456">doi:10.1101/491456</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/x2q7kmdi3vcbre5mrglhlwcfmy">fatcat:x2q7kmdi3vcbre5mrglhlwcfmy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190429140513/https://repository.kaust.edu.sa/bitstream/handle/10754/630282/491456.full.pdf;jsessionid=F9D9EC1AB800D4AFDBA19EFBAC5A038C?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6d/da/6dda3c4881d144ac04b22f17bdc32c7ed677e7ce.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/491456"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Novel algorithms for efficient subsequence searching and mapping in nanopore raw signals towards targeted sequencing

<span title="2020-03-01">2019</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
and accurately search and map genomic subsequences of interest in a pool of nanopore reads (or raw signals).  ...  Comprehensive experiments on real-world nanopore datasets show the efficiency and effectiveness of the proposed algorithms.  ...  Coin, Louise Roddam and Tania Duarte for providing the nanopore sequencing data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btz742">doi:10.1093/bioinformatics/btz742</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31593235">pmid:31593235</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cwdvlxjub5hglbj2an3o6q5m7a">fatcat:cwdvlxjub5hglbj2an3o6q5m7a</a> </span>
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An accurate and rapid continuous wavelet dynamic time warping algorithm for end-to-end mapping in ultra-long nanopore sequencing

Renmin Han, Yu Li, Xin Gao, Sheng Wang
<span title="2018-09-01">2018</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
One of the classic algorithms to solve the signal mapping problem is the dynamic time warping (DTW).  ...  Among various steps in nanopore data analysis, the end-to-end mapping between the raw electrical current signal sequence and the reference expected signal sequence serves as the key building block to signal  ...  Coin, Louise Roddam, and Tania Duarte for providing the nanopore sequencing data for the Pandoraea pnomenusa sample. We thank Haotian Teng for providing the code to draw the signal labeling figures.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bty555">doi:10.1093/bioinformatics/bty555</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30423085">pmid:30423085</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ktrql72e7beazj3adhew6ggfpu">fatcat:ktrql72e7beazj3adhew6ggfpu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200310135044/https://repository.kaust.edu.sa/bitstream/handle/10754/631196/cwDTW_ECCB2018_main.pdf;jsessionid=5FBB797F8B6370E2A55ADAAD0971A9D3?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/be/24/be2434bf5011e561095986e0230c49ee7974c26e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bty555"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

DeepSimulator: a deep simulator for Nanopore sequencing

Yu Li, Renmin Han, Chongwei Bi, Mo Li, Sheng Wang, Xin Gao, Bonnie Berger
<span title="2018-04-06">2018</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
task of which is the generation of raw electrical current signals.  ...  The reads generated by the default parameter have almost the same properties as the real data.  ...  Coin, Louise Roddam and Tania Duarte from University of Queensland for providing the nanopore sequencing data for the lambda phage, E. coli and Pandoraea pnomenusa samples.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bty223">doi:10.1093/bioinformatics/bty223</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29659695">pmid:29659695</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hi7acxx5mrcnraw4j4hfldrnbm">fatcat:hi7acxx5mrcnraw4j4hfldrnbm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190307195225/http://pdfs.semanticscholar.org/e62a/c7e9805bbe6c86898577a5fe41cc87cc069b.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e6/2a/e62ac7e9805bbe6c86898577a5fe41cc87cc069b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bty223"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a>

DeepSimulator: a deep simulator for Nanopore sequencing [article]

Yu Li, Renmin Han, Chongwei Bi, Mo Li, Sheng Wang, Xin Gao
<span title="2017-12-22">2017</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
task of which is the generation of raw electrical current signals.  ...  The reads generated by the default parameter have almost the same properties as the real data.  ...  Coin, Louise Roddam, and Tania Duarte for providing the nanopore sequencing data for the lambda phage, E. coli, and Pandoraea pnomenusa samples.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/238683">doi:10.1101/238683</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/c3yhl63qgvaubbvmenprlxm2ie">fatcat:c3yhl63qgvaubbvmenprlxm2ie</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190504003504/https://www.biorxiv.org/content/biorxiv/early/2018/01/03/238683.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/55/e6/55e69be0c69941df9700d4eef00ce7372aa8c23d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/238683"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

An accurate and rapid continuous wavelet dynamic time warping algorithm for unbalanced global mapping in nanopore sequencing [article]

Renmin Han, Yu Li, Sheng Wang, Xin Gao
<span title="2017-12-23">2017</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Among various steps in nanopore data analysis, the global mapping between the raw electrical current signal sequence and the expected signal sequence from the pore model serves as the key building block  ...  Meanwhile, on the real nanopore datasets, cwDTW is about 440 times faster than FastDTW and 3000 times faster than the original DTW. Our program is available at https://github.com/realbigws/cwDTW.  ...  Coin, Louise Roddam, and Tania Duarte for providing the nanopore sequencing data for the Pandoraea pnomenusa sample.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/238857">doi:10.1101/238857</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jqvhakzndvc2detnslqgvllu3m">fatcat:jqvhakzndvc2detnslqgvllu3m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190502001406/https://www.biorxiv.org/content/biorxiv/early/2017/12/23/238857.1.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f9/36/f93604fb692b6045b285497c8ca993b1b35cd0d1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/238857"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files

Alexander Payne, Nadine Holmes, Vardhman Rakyan, Matthew Loose, Inanc Birol
<span title="2018-11-20">2018</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Motivation: The Oxford Nanopore Technologies (ONT) MinION is used for sequencing a wide variety of sample types with diverse methods of sample extraction.  ...  Nanopore sequencers output FAST5 files containing signal data subsequently base called to FASTQ format.  ...  Conflict of Interest: ML was a member of the MinION access program and has received free flow cells and sequencing reagents in the past.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bty841">doi:10.1093/bioinformatics/bty841</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30462145">pmid:30462145</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hq4wdwzumnf6rbicncnksyxdxy">fatcat:hq4wdwzumnf6rbicncnksyxdxy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210717043811/https://nottingham-repository.worktribe.com/preview/1479051/bty841.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/13/54/1354480199ce1e47dfb80600cee8af94b9523964.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bty841"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

WaveNano: a signal-level nanopore base-caller via simultaneous prediction of nucleotide labels and move labels through bi-directional WaveNets

Sheng Wang, Zhen Li, Yizhou Yu, Xin Gao
<span title="2018-11-24">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rs7kqbk47nd3nbcl32zad56uv4" style="color: black;">Quantitative Biology</a> </i> &nbsp;
Despite the benefits of MinION to sequence ultra-long reads in real-time, the high error rate of the existing base-calling methods, especially indels (insertions and deletions), prevents its use in a variety  ...  Despite the benefits of this technique to sequence ultra-long reads in real-time, the high error rate of the existing base-calling methods, especially indels (insertions and deletions), prevents its use  ...  This article does not contain any studies with human or animal subjects performed by any of the authors.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s40484-018-0155-4">doi:10.1007/s40484-018-0155-4</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wvtefbkfenczhlueglmeomlafe">fatcat:wvtefbkfenczhlueglmeomlafe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190503023412/https://link.springer.com/content/pdf/10.1007%2Fs40484-018-0155-4.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/70/80/7080de75fadab48960130b30fc6ba93adcf6396c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s40484-018-0155-4"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis

Hasindu Gamaarachchi, Chun Wai Lam, Gihan Jayatilaka, Hiruna Samarakoon, Jared T. Simpson, Martin A. Smith, Sri Parameswaran
<span title="2020-08-05">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Nanopore sequencing enables portable, real-time sequencing applications, including point-of-care diagnostics and in-the-field genotyping.  ...  Achieving these outcomes requires efficient bioinformatic algorithms for the analysis of raw nanopore signal data.  ...  Acknowledgements We thank NVIDIA for providing the Jetson TX2 board (to University of New South Wales) and Tesla K40 GPU (to University of Peradeniya) through the GPU donation programme. We thank Dr.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-020-03697-x">doi:10.1186/s12859-020-03697-x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32758139">pmid:32758139</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/k4ylm4rwy5ejnip3lgrlq4qh2a">fatcat:k4ylm4rwy5ejnip3lgrlq4qh2a</a> </span>
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NanoSPC: a scalable, portable, cloud compatible viral nanopore metagenomic data processing pipeline

Yifei Xu, Fan Yang-Turner, Denis Volk, Derrick Crook
<span title="2020-05-22">2020</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Metagenomic sequencing combined with Oxford Nanopore Technology has the potential to become a point-of-care test for infectious disease in public health and clinical settings, providing rapid diagnosis  ...  Here we introduce NanoSPC, a scalable, portable and cloud compatible pipeline for analyzing Nanopore sequencing data.  ...  METHODS AND FUNCTIONALITIES Data input and quality control NanoSPC takes Nanopore sequencing reads of the fastq format and, optionally, raw signal data of the fast5 format as input ( Figure 1 ).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkaa413">doi:10.1093/nar/gkaa413</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32442274">pmid:32442274</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6dtk4z4yqjdtjnocm3xnjozsia">fatcat:6dtk4z4yqjdtjnocm3xnjozsia</a> </span>
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DeepNano-blitz: A Fast Base Caller for MinION Nanopore Sequencers [article]

Vladimir Boza, Peter Peresini, Brona Brejova, Tomas Vinar
<span title="2020-02-12">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Current base callers, however, require a powerful GPU to analyze data produced by MinION in real time, which hampers field applications.  ...  of results for more detailed analysis (i.e. filtering out human DNA from human--pathogen runs).  ...  It allows trading accuracy for speed and enables real-time data analysis without requirement of a powerful GPU.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.02.11.944223">doi:10.1101/2020.02.11.944223</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/an67httssvdq7d6qqzb3djhlxe">fatcat:an67httssvdq7d6qqzb3djhlxe</a> </span>
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Nanopore basecalling from a perspective of instance segmentation

Yao-zhong Zhang, Arda Akdemir, Georg Tremmel, Seiya Imoto, Satoru Miyano, Tetsuo Shibuya, Rui Yamaguchi
<span title="2020-04-23">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Nanopore sequencing is a rapidly developing third-generation sequencing technology, which can generate long nucleotide reads of molecules within a portable device in real-time.  ...  Through detecting the change of ion currency signals during a DNA/RNA fragment's pass through a nanopore, genotypes are determined.  ...  The super-computing resource was provided by Human Genome Center, the Institute of Medical Science, the University of Tokyo.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-020-3459-0">doi:10.1186/s12859-020-3459-0</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32321433">pmid:32321433</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/c5tj2ugo5zgotawyohngfn6yee">fatcat:c5tj2ugo5zgotawyohngfn6yee</a> </span>
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Whale watching with BulkVis: A graphical viewer for Oxford Nanopore bulk fast5 files [article]

Alex Payne, Nadine Holmes, Vardhman Rakyan, Matthew Loose
<span title="2018-05-03">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Motivation: The Oxford Nanopore Technologies (ONT) MinION is used for sequencing a wide variety of sample types with diverse methods of sample extraction.  ...  Nanopore sequencers output fast5 files containing signal data subsequently base called to fastq format.  ...  The real time nature of nanopore sequencing means that reads are written to disk as soon as the DNA has translocated through the pore.  ... 
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