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SOAP2: an improved ultrafast tool for short read alignment

R. Li, C. Yu, Y. Li, T.-W. Lam, S.-M. Yiu, K. Kristiansen, J. Wang
<span title="2009-06-03">2009</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;
SOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate.  ...  A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome. Availability: http://soap.  ...  ACKNOWLEDGEMENTS We are indebted to the many SOAP users who tested the program, reported bugs and proposed improvements to make it more powerful and user friendly.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btp336">doi:10.1093/bioinformatics/btp336</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19497933">pmid:19497933</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cx4bkb2ffjh43dqdfxakhr53ga">fatcat:cx4bkb2ffjh43dqdfxakhr53ga</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20141212122321/http://bioinformatics.oxfordjournals.org:80/content/25/15/1966.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/e9/e9/e9e9a7c6b7d6d9a5c343d70ebc640091848baca6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btp336"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

A Comprehensive Evaluation of Alignment Algorithms in the Context of RNA-Seq

Robert Lindner, Caroline C. Friedel, Steven L. Salzberg
<span title="2012-12-26">2012</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;
Here, special emphasis was placed on both precision and recall and the performance for different read lengths and numbers of mismatches and indels in a read.  ...  In recent years, a large number of such mapping algorithms have been developed, all of which have in common that they require algorithms for aligning a vast number of reads to genomic or transcriptomic  ...  Contributed reagents/ materials/analysis tools: RL. Wrote the paper: RL CCF.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0052403">doi:10.1371/journal.pone.0052403</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23300661">pmid:23300661</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3530550/">pmcid:PMC3530550</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/63tm7c2e4zgljeamjrlen5kgka">fatcat:63tm7c2e4zgljeamjrlen5kgka</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171005174756/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0052403&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/ae/c0/aec0037ac32f955f2902dfe5991abea51ba7689e.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.0052403"> <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/PMC3530550" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Computational and Bioinformatics Frameworks for Next-Generation Whole Exome and Genome Sequencing

Marisa P. Dolled-Filhart, Michael Lee, Chih-wen Ou-yang, Rajini Rani Haraksingh, Jimmy Cheng-Ho Lin
<span title="">2013</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nxzqpsogkbe55mjq33syzghf2e" style="color: black;">The Scientific World Journal</a> </i> &nbsp;
Furthermore, we discuss possible future developments as data sources grow and highlight opportunities for new bioinformatics tools to be developed.  ...  For each of the three stages of (1) alignment, (2) variant calling, and (3) filtering and annotation, we describe the analysis required and survey the different software packages that are used.  ...  Louis, VarScan (http:// genome.wustl.edu/tools/cancer-genomics/) is an open source tool for short read variant detection of SNPs and indels that is compatible with multiple sequencing platforms and aligner  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2013/730210">doi:10.1155/2013/730210</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23365548">pmid:23365548</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3556895/">pmcid:PMC3556895</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7n6pbn3lqbf55pmugg3pwrjdkm">fatcat:7n6pbn3lqbf55pmugg3pwrjdkm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190224192841/http://pdfs.semanticscholar.org/5a1b/61b78f3f50d642c703668339f6c9ff54a02d.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/5a/1b/5a1b61b78f3f50d642c703668339f6c9ff54a02d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2013/730210"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> hindawi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3556895" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Analysis of Genotyping-by-Sequencing (GBS) Data [chapter]

Sateesh Kagale, Chushin Koh, Wayne E. Clarke, Venkatesh Bollina, Isobel A. P. Parkin, Andrew G. Sharpe
<span title="">2016</span> <i title="Springer New York"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6v4flwr6afbfrmhdyu6xe3dyvm" style="color: black;">Msphere</a> </i> &nbsp;
Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) is an ultrafast short read alignment tool that can be used for aligning sequencing reads against a reference genome [21] .  ...  Most of these widely used aligners utilize hashing algorithms (MAQ, mrsFast, STAMPY) or Burrows-Wheeler transform (BWT) [37] based indexing (Bowtie2, BWA and SOAP2) for short read mapping.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-4939-3167-5_15">doi:10.1007/978-1-4939-3167-5_15</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26519412">pmid:26519412</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uztdsr6f5nbfln62rgjlte5leq">fatcat:uztdsr6f5nbfln62rgjlte5leq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190427105937/https://nrc-publications.canada.ca/eng/view/author/version/?id=2ebe20b9-f190-4f15-a0a5-a8789df676f1" 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/90/fe/90fe7e530be0f1743a7c9ee9f9b86948e27ad09e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-4939-3167-5_15"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Mapping and differential expression analysis from short-read RNA-Seq data in model organisms

Qiong-Yi Zhao, Jacob Gratten, Restuadi Restuadi, Xuan Li
<span title="">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rs7kqbk47nd3nbcl32zad56uv4" style="color: black;">Quantitative Biology</a> </i> &nbsp;
For model organisms with a reference genome, the first step in analysis of RNA-Seq data involves mapping of short-read sequences to the reference genome.  ...  Reference-guided transcriptome assembly is an optional step, which is recommended if the aim is to identify novel transcripts.  ...  Jennifer Whitehead for critical reading of the manuscript. This work is supported by the National Health and Medical Research Council project grants (Nos.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s40484-016-0060-7">doi:10.1007/s40484-016-0060-7</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/idomdo4pdjgr3o7jvz44w2uxlu">fatcat:idomdo4pdjgr3o7jvz44w2uxlu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180723145800/https://link.springer.com/content/pdf/10.1007%2Fs40484-016-0060-7.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/03/21/0321277baa8f925d687c6cc1826c6ba132fa6b14.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s40484-016-0060-7"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Bioinformatics Approaches for the Identification and Annotation of RNA Editing Sites

Soo Youn Lee, Ju Han Kim
<span title="2013-06-30">2013</span> <i title="Korean Society of Medical Genetics"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/vpq2tvbej5hz5eahst5hbhtrmm" style="color: black;">Journal of Genetic Medicine</a> </i> &nbsp;
Accordingly, many bioinformatics tools and algorithms to identify novel RNA editing sites and semantic annotation of known information are increasingly being introduced.  ...  This review summarizes modern bioinformatics approaches and related resources for RNA editing research.  ...  Bowtie is a fast, memoryefficient short read aligner, aligning short DNA reads to the human genome at a rate of over 25 million 35-bp reads per hour.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5734/jgm.2013.10.1.27">doi:10.5734/jgm.2013.10.1.27</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2vwqfkw25zfs7bv2f7pv5rcmgy">fatcat:2vwqfkw25zfs7bv2f7pv5rcmgy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809033558/http://www.snubi.org/~juhan/pubFiles/RNAEditing.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/fc/50/fc505fd292604b395d7a7a80c4d60b107554e0eb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5734/jgm.2013.10.1.27"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </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;
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.  ...  sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths.  ...  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>

Technology dictates algorithms: Recent developments in read alignment [article]

Mohammed Alser, Jeremy Rotman, Kodi Taraszka, Huwenbo Shi, Pelin Icer Baykal, Harry Taegyun Yang, Victor Xue, Sergey Knyazev, Benjamin D. Singer, Brunilda Balliu, David Koslicki, Pavel Skums (+4 others)
<span title="2020-07-09">2020</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Our review provides a survey of algorithmic foundations and methodologies across 107 alignment methods published between 1988 and 2020, for both short and long reads.  ...  Aligning reads onto reference genomes enables the identification of individual-specific genetic variants and is an essential step of the majority of genomic analysis pipelines.  ...  Highly sensitive and ultrafast read mapping for RNA-seq analysis. DNA Res. 23, 93-100 (2016). 59. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2003.00110v3">arXiv:2003.00110v3</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3l3ad4z5xfhjxoo7snaskartxi">fatcat:3l3ad4z5xfhjxoo7snaskartxi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200929235205/https://arxiv.org/ftp/arxiv/papers/2003/2003.00110.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/c9/13/c9139d44b1a0667e908c502690cd4785ef1cbb7f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2003.00110v3" 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>

Gene mapping of nine agronomic traits and genome assembly by resequencing a foxtail millet RIL population [article]

Xuemei NI, Qiuju Xia, Shu Cheng, Hui Li, Guangyu Fan, Houbao Zhang, Tao Guo, Ping Huang, Haitao Xiang, Qingchun Chen, Ning Li, Hongfeng Zou (+7 others)
<span title="2016-08-15">2016</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The genome resequencing and QTL mapping provided important tools for foxtail millet research and breeding.  ...  Resequencing of the RILs could also provide an effective way for high quantity genome assembly and gene identification.  ...  ., 2009 The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079. LI, R., C. YU, Y. LI, T. W. LAM, S. M. YIU et al., 2009 SOAP2: an improved ultrafast G. Y., X. LIU, Z. W.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/069625">doi:10.1101/069625</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/d7lmp5bjqbg4bemkp4hp4gqeji">fatcat:d7lmp5bjqbg4bemkp4hp4gqeji</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190502095102/https://www.biorxiv.org/content/biorxiv/early/2016/08/15/069625.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/54/b5/54b56b4bc341d01e51bbda270a2409c7e9d446a3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/069625"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Advanced Applications of RNA Sequencing and Challenges

Yixing Han, Shouguo Gao, Kathrin Muegge, Wei Zhang, Bing Zhou
<span title="">2015</span> <i title="SAGE Publications"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/i7e77v75qbe7rbbcdp63ijxhza" style="color: black;">Bioinformatics and Biology Insights</a> </i> &nbsp;
RNA-seq is now being used widely for uncovering multiple facets of transcriptome to facilitate the biological applications.  ...  Specifically, we discuss essential principles of computational methods that are required to meet the key challenges of the RNA-seq data analyses, development of various bioinformatics tools, challenges  ...  Cuncong Zhong for suggestions on the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4137/bbi.s28991">doi:10.4137/bbi.s28991</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26609224">pmid:26609224</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4648566/">pmcid:PMC4648566</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fhaqier5frev7eer6s6fn3pqse">fatcat:fhaqier5frev7eer6s6fn3pqse</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170812025944/http://insights.sagepub.com/redirect_file.php?fileId=6957&amp;filename=5204-BBI-Advanced-Applications-of-RNA-Sequencing-and-Challenges.pdf&amp;fileType=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/37/57/37573fdabf35cb001064447289b02bc42b7aebf2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4137/bbi.s28991"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4648566" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

libgapmis: extending short-read alignments

Nikolaos Alachiotis, Simon Berger, Tomáš Flouri, Solon P Pissis, Alexandros Stamatakis
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Results: In this article, we present libgapmis, a library for extending pairwise short-read alignments.  ...  After aligning a substring of the reference sequence against the high-quality prefix of a short read-the seed-an important problem is to find the best possible alignment between a substring of the reference  ...  Acknowledgements The publication costs for this article were funded by the Heidelberg Institute for Theoretical Studies (HITS gGmbH).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-14-s11-s4">doi:10.1186/1471-2105-14-s11-s4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24564250">pmid:24564250</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3821552/">pmcid:PMC3821552</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/e2nwch7u3zfatf62lmjazamswq">fatcat:e2nwch7u3zfatf62lmjazamswq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720094140/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-14-S11-S4?site=bmcbioinformatics.biomedcentral.com" 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/b5/c6/b5c6d3e4960f51591f3392b6f61b1eba06c31e20.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-14-s11-s4"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3821552" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The Theory and Practice of Genome Sequence Assembly

Jared T. Simpson, Mihai Pop
<span title="2015-08-24">2015</span> <i title="Annual Reviews"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/76paa6gbdzdsdhhe62uk3giv3m" style="color: black;">Annual review of genomics and human genetics (Print)</a> </i> &nbsp;
sophisticated computational tools called genome assemblers (short for genome sequence assemblers).  ...  For personal use only.  ...  SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25:1966-67 58. Lippert RA. 2005. Space-efficient whole genome comparisons with Burrows-Wheeler transforms. J. Comput.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1146/annurev-genom-090314-050032">doi:10.1146/annurev-genom-090314-050032</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25939056">pmid:25939056</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iayzwkwyljey5nn6hyxhwgsg7u">fatcat:iayzwkwyljey5nn6hyxhwgsg7u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190220092158/http://pdfs.semanticscholar.org/21b3/df4742aeb80d6393c4bd7c14d4e5450a6ba0.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/21/b3/21b3df4742aeb80d6393c4bd7c14d4e5450a6ba0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1146/annurev-genom-090314-050032"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Ultrafast clustering algorithms for metagenomic sequence analysis

W. Li, L. Fu, B. Niu, S. Wu, J. Wooley
<span title="2012-07-06">2012</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
DATABASE SEARCH In metagenomic projects, an important annotation step is to query the reads or Open Reading Frames (ORF) against reference databases of known genomes, DNAs or proteins with an alignment  ...  Herein, we show an example using clusteringbased filtering to improve metagenome assembly.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbs035">doi:10.1093/bib/bbs035</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22772836">pmid:22772836</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3504929/">pmcid:PMC3504929</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dt4day4wqvfmdg2dl35ofojs3a">fatcat:dt4day4wqvfmdg2dl35ofojs3a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170716163326/https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bib/13/6/10.1093/bib/bbs035/2/bbs035.pdf?Expires=1500316406&amp;Signature=bhlWBbz7P2YqD8YlGOBh77Dj15pxq0ig5gSKYzj9NFxeTndlKMot5zqbFsyXrssLJ~Fm51Mz4Xypo~L~u3nYK00u5SgtKIwLQwYJqsZhLMil-G2HbMaz3w~7-T3ybhTQ13gH4BmwnM~nAlgfR8-5Lg3MlhMe-3yqyzxELxCBUwHJH8iIzyJq24a2Rc1Q46z1XUNh9us~6YfIyCDOxofmq4qL4qyh8hbkhnmrFaKTd-XneFcCvS~kexrRvQpr94X4vsAGHGxgu~dZUsKOcNABIL-v4yu8ku1lriFmRUCfvhbPfXQit6cnxBPOIYHdtHMuDmK406x5DeeVPDbBRTigHA__&amp;Key-Pair-Id=APKAIUCZBIA4LVPAVW3Q" 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/55/4c/554c30aa802b41586d8ee35a864275ba7ed0fcb1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbs035"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3504929" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Transcriptomic Profiling Using Next Generation Sequencing - Advances, Advantages, and Challenges [chapter]

Krishanpal Anamika, Srikant Verma, Abhay Jere, Aarti Desai
<span title="2016-01-14">2016</span> <i title="InTech"> Next Generation Sequencing - Advances, Applications and Challenges </i> &nbsp;
Each of these RNA molecules plays a vital role in the physiological response, and understanding the regulation of these molecules is extremely critical for the better understanding of the functional genome  ...  This chapter describes the significance of RNASeq study over arraybased traditional methods, approach to analyze RNASeq data, available methods and tools, challenges associated with the data analysis,  ...  Multiple aligners, which can be divided into two categories, are available for aligning short-reads to the genome: 1.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/61789">doi:10.5772/61789</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/psftl6dwxnc6rpxq6ho2jqz7ru">fatcat:psftl6dwxnc6rpxq6ho2jqz7ru</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190427101853/https://cdn.intechopen.com/pdfs/49525.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/16/bd/16bdd81c836baf1a8e99b92e635fcd1ad3c75177.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/61789"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism

Isiaka Ibrahim Muhammad, Sze Ling Kong, Siti Nor Akmar Abdullah, Umaiyal Munusamy
<span title="2019-12-25">2019</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3loumxx7kzamnlu4h6x3xoz6ay" style="color: black;">International Journal of Molecular Sciences</a> </i> &nbsp;
It also provides guidelines for making choices in selecting specific protocols in RNA-seq pipelines for genome-wide analysis to achieve more detailed characterization of specific transcription regulatory  ...  This review discusses recent advances in methods for studying transcriptional regulation using these two methods.  ...  TopHat utilizes Bowtie as an alignment "engine" to map millions of RNA-seq reads to the genome and these read alignments serve as input for Cufflinks to produce a transcriptome assembly for each condition  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms21010167">doi:10.3390/ijms21010167</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31881735">pmid:31881735</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6981605/">pmcid:PMC6981605</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yv25lasn65cnrpkho2bx5asbgy">fatcat:yv25lasn65cnrpkho2bx5asbgy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191226011311/https://res.mdpi.com/d_attachment/ijms/ijms-21-00167/article_deploy/ijms-21-00167.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/20/b7/20b72bc5f378ed7cd3fcb58b32b5e296af9d1248.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms21010167"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6981605" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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