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SOAP3: ultra-fast GPU-based parallel alignment tool for short reads

C.-M. Liu, T. Wong, E. Wu, R. Luo, S.-M. Yiu, Y. Li, B. Wang, C. Yu, X. Chu, K. Zhao, R. Li, T.-W. Lam
<span title="2012-01-28">2012</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;
SOAP3 is the first short read alignment tool that leverages the multi-processors in a graphic processing unit (GPU) to achieve a drastic improvement in speed.  ...  For aligning reads with up to 4 mismatches, SOAP3 aligns slightly more reads than BWA and Bowtie; this is because SOAP3, unlike BWA and Bowtie, is not heuristic-based and always reports all answers.  ...  We would like to thank the users of SOAP3 (in particular, BGI and NIH) for their support and feedbacks.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bts061">doi:10.1093/bioinformatics/bts061</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22285832">pmid:22285832</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/umqxsgb3bjcv7akyf6uydjxcf4">fatcat:umqxsgb3bjcv7akyf6uydjxcf4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20140514020221/http://bioinformatics.oxfordjournals.org:80/content/early/2012/01/28/bioinformatics.bts061.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/e6/5d/e65d3655b94742139540eef98a659ae033d2580f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bts061"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner

Ruibang Luo, Thomas Wong, Jianqiao Zhu, Chi-Man Liu, Xiaoqian Zhu, Edward Wu, Lap-Kei Lee, Haoxiang Lin, Wenjuan Zhu, David W. Cheung, Hing-Fung Ting, Siu-Ming Yiu (+6 others)
<span title="2013-05-31">2013</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, GEM and GPU-based aligners including BarraCUDA and CUSHAW, SOAP3-dp is two to tens of times faster, while maintaining the highest  ...  To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity.  ...  Acknowledgments We thank the four anonymous reviewers for their professional and constructive suggestions. Author Contributions Wrote the paper: TL R. Luo TW. Contributed equally to this work: R.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0065632">doi:10.1371/journal.pone.0065632</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23741504">pmid:23741504</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3669295/">pmcid:PMC3669295</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2jztxxmdhfgodpunb6d5xnq6jy">fatcat:2jztxxmdhfgodpunb6d5xnq6jy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171007085434/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0065632&amp;type=printable" 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/46/2d/462dbf6656a504ebe5b0664f94f302dd5e0233c6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0065632"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3669295" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Short Read Mapping: An Algorithmic Tour

Stefan Canzar, Steven L. Salzberg
<span title="">2017</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/yfvtieuumfamvmjlc255uckdlm" style="color: black;">Proceedings of the IEEE</a> </i> &nbsp;
Although optimal alignment algorithms to solve this problem have long been available, the practical requirements of aligning hundreds of millions of short reads to the 3 billion base pair long human genome  ...  Other methods for fast indexing also emerged at this time, such as the BLAT [50] and SSAHA [93] programs, both of which (similarly to FASTA) used a hash index based on ktuples.  ...  Hashing-Based GPU Aligners Blom et al. [11] developed SARUMAN, the first short read aligner that makes use of GPU computing power.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/jproc.2015.2455551">doi:10.1109/jproc.2015.2455551</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28502990">pmid:28502990</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5425171/">pmcid:PMC5425171</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ic6d6z5ggbazdkaotcotdtbo3u">fatcat:ic6d6z5ggbazdkaotcotdtbo3u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200503234007/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5425171&amp;blobtype=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/97/3f/973f07bd295ae212830610753dd791053f9ff9c9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/jproc.2015.2455551"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5425171" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

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

Hasindu Gamaarachchi
<span title="2021-01-13">2021</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Consequently, the full utility of an ultra-portable sequencer for sequencing in-the-field or at the point-of-care is limited by the lack of portable lightweight analytic techniques.  ...  The optimised software tools are used in complete end-to-end analysis workflows and their efficacy is demonstrated by running on prototypical embedded systems.  ...  Earlier short-read alignment tools used the hash table-based approach.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2101.05012v1">arXiv:2101.05012v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wcujdqliwzgrxd2zc2wcudbqpu">fatcat:wcujdqliwzgrxd2zc2wcudbqpu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210118034409/https://arxiv.org/pdf/2101.05012v1.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/6a/0e/6a0e35bb8085b364a5449cebfad3f9ea0ae79860.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2101.05012v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Novel Computational Techniques For Mapping And Classifying Next-Generation Sequencing Data

Karel Břinda, Gregory Kucherov, Valentina Boeva
<span title="2016-11-28">2016</span> <i title="Zenodo"> Zenodo </i> &nbsp;
Dynamic mapping is based on exploiting the information from previously computed alignments, helping to improve the mapping of subsequent reads.  ...  In this thesis, we present novel computational techniques for read mapping and taxonomic classification. With more than a hundred of published mappers, read mapping might be considered fully solved.  ...  , G-Aligner [411] , GPU-BWT [412] , SOAP3 [413] ; SARUMAN [414] ; CUDAlign [415] , GPU-RMAP [416] , and MUM-merGPU [417]  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.1045317">doi:10.5281/zenodo.1045317</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/agbwpocisncwvihn2ij5q3ongq">fatcat:agbwpocisncwvihn2ij5q3ongq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201224062120/https://zenodo.org/record/1045317/files/brinda_phd.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/ec/18/ec185aa259e4a4f0a7fa73b54ed50cd57b072712.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.1045317"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>

A Survey on Sequence Alignment Based on Hadoop/MapReduce Big Data

Prabhat Gupta, Rajeev Pandey, Anjna Deen
<span class="release-stage">unpublished</span>
We additionally consider future advancement of MSA techniques with connection to applying of all the more entirely unexpected advances and consequently the possibility of parallelization of MSA.  ...  All of those algorithms have demonstrated their potential to unravel several alignment issues.  ...  Cloud Aligner A MapReduce based approch for mapping short reads created by next-generation sequencing [9] Cloud Burst A parallel read-mapping algorith m for mapping next-generation sequence data to the  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nhvl7utofzfp7nbx745o3xu5xq">fatcat:nhvl7utofzfp7nbx745o3xu5xq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180423044828/http://www.ijcta.com/documents/volumes/vol8issue4/ijcta2017080402.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/55/56/5556ce8ffb31895f3f13de426a292d3ac64d1373.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a>

Genome-wide identification of binding sites of GRHL2 in luminal-like and basal A subtypes of breast cancer [article]

Erik HJ Danen, Zi Wang, Haoyu Wu, Lucia Daxinger
<span title="2020-02-14">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
For luminal-like cells, 6,527 common binding sites were identified, of which 208 binding sites were found in gene promoter regions.  ...  The identified GRHL2-binding motifs are all identical to a motif reported for human ovarian cancer, indicating conserved GRHL2 DNA-binding among human cancer cells.  ...  ., SOAP3: ultra-fast GPU-based parallel alignment tool for short reads. 2012. 28(6): p. 878-879. 22. Ewing, B., et al., Base-calling of automated sequencer traces using phred. I.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.02.13.946947">doi:10.1101/2020.02.13.946947</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zroyzecgpzgehefdcpv3fgzy6q">fatcat:zroyzecgpzgehefdcpv3fgzy6q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200216025455/https://www.biorxiv.org/content/biorxiv/early/2020/02/14/2020.02.13.946947.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] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.02.13.946947"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>