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Faster Algorithms for 1-Mappability of a Sequence [chapter]

Mai Alzamel, Panagiotis Charalampopoulos, Costas S. Iliopoulos, Solon P. Pissis, Jakub Radoszewski, Wing-Kin Sung
<span title="">2017</span> <i title="Springer International Publishing"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
In the k-mappability problem, we are given a string x of length n and integers m and k, and we are asked to count, for each length-m factor y of x, the number of other factors of length m of x that are  ...  We focus here on the version of the problem where k = 1. The fastest known algorithm for k = 1 requires time O(mn log n/ log log n) and space O(n).  ...  The aim from a biological perspective is to compute the mappability of each region of a genome sequence; i.e. for every factor of a given length of the sequence, we are asked to count how many other times  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-319-71147-8_8">doi:10.1007/978-3-319-71147-8_8</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hgqbvfm24bep5p67yqx2z5b5xa">fatcat:hgqbvfm24bep5p67yqx2z5b5xa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190225080050/http://pdfs.semanticscholar.org/5ce5/3033d1c2ea8f530d5604316d68d3e9cc55f7.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/5c/e5/5ce53033d1c2ea8f530d5604316d68d3e9cc55f7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-319-71147-8_8"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Faster algorithms for 1-mappability of a sequence [article]

Mai Alzamel, Panagiotis Charalampopoulos, Costas S. Iliopoulos, Solon P. Pissis, Jakub Radoszewski, Wing-Kin Sung
<span title="2017-05-11">2017</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
In the k-mappability problem, we are given a string x of length n and integers m and k, and we are asked to count, for each length-m factor y of x, the number of other factors of length m of x that are  ...  We focus here on the version of the problem where k = 1. The fastest known algorithm for k = 1 requires time O(mn log n/ log log n) and space O(n).  ...  The aim from a biological perspective is to compute the mappability of each region of a genome sequence; i.e. for every factor of a given length of the sequence, we are asked to count how many other times  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1705.04022v1">arXiv:1705.04022v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xh4iqa7ufvbgzfgofmizebfiie">fatcat:xh4iqa7ufvbgzfgofmizebfiie</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191018112751/https://arxiv.org/pdf/1705.04022v1.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/80/19/8019810320c35915bd345406ee2b3e1c4803b680.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1705.04022v1" 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>

GenMap: Fast and Exact Computation of Genome Mappability [article]

Christopher Pockrandt, Mai Alzamel, Costas S. Iliopoulos, Knut Reinert
<span title="2019-04-26">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We present a fast and exact algorithm to compute the (k,e)-mappability. Its inverse, the (k,e)-frequency counts the number of occurrences of each k-mer with up to e errors in a sequence.  ...  The algorithm we present is a magnitude faster than the algorithm in the widely used GEM suite while not relying on heuristics, and can even compute the mappability for short k-mers on highly repetitive  ...  Acknowledgements The authors acknowledge the support of the de.NBI network for bioinformatics infrastructure, the Intel SeqAn IPCC and the IMPRS for Computational Biology and Scientific Computing.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/611160">doi:10.1101/611160</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/h7vr3jtvezaxjpywrblg52sjwm">fatcat:h7vr3jtvezaxjpywrblg52sjwm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200711012504/https://www.biorxiv.org/content/biorxiv/early/2019/04/26/611160.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/bf/bb/bfbbfa6537ff7e8555d1d78af2c388c0fec720c9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/611160"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

GenMap: Ultra-fast Computation of Genome Mappability

Christopher Pockrandt, Mai Alzamel, Costas S Iliopoulos, Knut Reinert, Jinbo Xu
<span title="2020-04-04">2020</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;
This allows for the computation of marker sequences or finding candidates for probe design by identifying approximate k-mers that are unique to a genome or that are present in all genomes.  ...  We extend the mappability algorithm, such that it can also be computed across multiple genomes where a k-mer occurrence is only counted once per genome.  ...  Acknowledgements The authors acknowledge the support of the de.NBI network for bioinformatics infrastructure, the Intel SeqAn IPCC and the IMPRS for Computational Biology and Scientific Computing.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btaa222">doi:10.1093/bioinformatics/btaa222</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32246826">pmid:32246826</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7320602/">pmcid:PMC7320602</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nlhqhjtokzbanimmj5zsnviite">fatcat:nlhqhjtokzbanimmj5zsnviite</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201108032526/https://pure.mpg.de/rest/items/item_3222831_1/component/file_3222832/content" 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/3b/9e/3b9e087d5f0cf0d955be9ffd64cabf6501776741.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btaa222"> <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/PMC7320602" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

FANSe2: A Robust and Cost-Efficient Alignment Tool for Quantitative Next-Generation Sequencing Applications

Chuan-Le Xiao, Zhi-Biao Mai, Xin-Lei Lian, Jia-Yong Zhong, Jing-jie Jin, Qing-Yu He, Gong Zhang, Zhang Zhang
<span title="2014-04-17">2014</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;
Correct and bias-free interpretation of the deep sequencing data is inevitably dependent on the complete mapping of all mappable reads to the reference sequence, especially for quantitative RNA-seq applications  ...  We implemented a scalable and almost maintenance-free parallelization method that can utilize the computational power of multiple office computers, a novel feature not present in any other mainstream algorithm  ...  Hanqi Yin (Shanghai Biotechnology Corporation) for his help on analyzing the microarray data. Author Contributions  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0094250">doi:10.1371/journal.pone.0094250</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24743329">pmid:24743329</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3990525/">pmcid:PMC3990525</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rsozob7ut5brfb3oglu2rjhmli">fatcat:rsozob7ut5brfb3oglu2rjhmli</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC3990525/PMC3990525-journal.pone.0094250.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> File Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/27/b9/27b928aeb816bd928591e8ff54325d9e1981ba48.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0094250"> <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/PMC3990525" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

BiSpark: a Spark-based highly scalable aligner for bisulfite sequencing data

Seokjun Soe, Yoonjae Park, Heejoon Chae
<span title="">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
However, a dearth of efficient aligner that is designed for bisulfite-treated sequencing becomes a bottleneck of large-scale DNA methylome analyses.  ...  Results: In this study, we present a highly scalable, efficient, and load-balanced bisulfite aligner, BiSpark, which is designed for processing large volumes of bisulfite sequencing data.  ...  Availability of data and materials The implementation of BiSpark software package, source code, and test data sets are available at https://bhi-kimlab.github.io/BiSpark/.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-018-2498-2">doi:10.1186/s12859-018-2498-2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fyolmxaegnds7bqiwtp4pityge">fatcat:fyolmxaegnds7bqiwtp4pityge</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190426105729/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2498-2" 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/e8/85/e885e091120df820db5d7473875826bc289a9eee.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-018-2498-2"> <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>

MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data

Parameswaran Ramachandran, Gareth A. Palidwor, Christopher J. Porter, Theodore J. Perkins
<span title="2013-01-07">2013</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
Motivation: Reliable estimation of the mean fragment length for next-generation short-read sequencing data is an important step in next-generation sequencing analysis pipelines, most notably because of  ...  We propose a new approach, called mappability-sensitive cross-correlation (MaSC), which removes this bias and allows for accurate and reliable fragment-length estimation.  ...  ACKNOWLEDGEMENT The authors gratefully acknowledge Dr Michael Rudnicki and Dr Vahab Soleimani for data and discussions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btt001">doi:10.1093/bioinformatics/btt001</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23300135">pmid:23300135</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3570216/">pmcid:PMC3570216</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2g6xschejnaurpshsbqkuvr2rm">fatcat:2g6xschejnaurpshsbqkuvr2rm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180721021021/https://ruor.uottawa.ca/bitstream/10393/24088/1/Ramachandran_Parameswaran_2013_MaSC_mappabilty-sensitive_cross-correlation.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/ea/a4/eaa4e9f2e6772971c9be1a206ffc87bf485bbd52.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btt001"> <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/PMC3570216" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain

<span title="2019-07-15">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;
TideHunter is tens of times faster than state-of-the-art methods and has a higher sensitivity and accuracy.  ...  By integrating additional in silico processing steps, these tandem sequences can be collapsed into a consensus sequence with a higher accuracy than the original raw reads.  ...  Funding This study was supported by a startup fund from the Children's Hospital of Philadelphia.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btz376">doi:10.1093/bioinformatics/btz376</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31510677">pmid:31510677</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6612900/">pmcid:PMC6612900</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sacm3omjjfc45gjfvrk6dcyrqe">fatcat:sacm3omjjfc45gjfvrk6dcyrqe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200502001653/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6612900&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/45/aa/45aacfd35dbd26df00bc643f2cb8500d170b0b97.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btz376"> <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/PMC6612900" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

From Wet-Lab to Variations: Concordance and Speed of Bioinformatics Pipelines for Whole Genome and Whole Exome Sequencing

Steve Laurie, Marcos Fernandez-Callejo, Santiago Marco-Sola, Jean-Remi Trotta, Jordi Camps, Alejandro Chacón, Antonio Espinosa, Marta Gut, Ivo Gut, Simon Heath, Sergi Beltran
<span title="2016-09-26">2016</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2vzjuzyygveinhd4ab2ux34qv4" style="color: black;">Human Mutation</a> </i> &nbsp;
As whole genome sequencing becomes cheaper and faster, it will progressively substitute targeted next-generation sequencing as standard practice in research and diagnostics.  ...  We report differences in speed of up to 20 times in some steps of the process and have observed that SNV, and to a lesser extent InDel, detection is highly consistent in 70% of the genome.  ...  Acknowledgments We thank Raul Tonda for help with pipeline implementation and figure generation, and Nvidia for their donation of part of the systems used in this work.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/humu.23114">doi:10.1002/humu.23114</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27604516">pmid:27604516</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5129537/">pmcid:PMC5129537</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5nsmszxr6bhi5dp6j63oh7m5fe">fatcat:5nsmszxr6bhi5dp6j63oh7m5fe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200311012226/https://repositori.upf.edu/bitstream/handle/10230/30879/Gut_hummut_from.pdf;jsessionid=A1173BCD2FBC41D6B1048BD8DB7EF0C0?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/27/e2/27e27ee5f0fdb974eb5b1982bcedf85bea7589e7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/humu.23114"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5129537" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data

Dongjun Chung, Pei Fen Kuan, Bo Li, Rajendran Sanalkumar, Kun Liang, Emery H. Bresnick, Colin Dewey, Sündüz Keleş, Wyeth W. Wasserman
<span title="2011-07-14">2011</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
identifiable with unireads, and improves detection of peaks in mappable regions.  ...  The state of the art for analyzing ChIP-seq data relies on using only reads that map uniquely to a relevant reference genome (uni-reads).  ...  Acknowledgments We acknowledge Xin Zeng's assistance with the calculation of mappability scores for 75 mer SETs and thank Prof.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1002111">doi:10.1371/journal.pcbi.1002111</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21779159">pmid:21779159</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3136429/">pmcid:PMC3136429</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/urnfshc36rfpdd7t6u6yt6hlo4">fatcat:urnfshc36rfpdd7t6u6yt6hlo4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171015134036/http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002111&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/9a/43/9a43f8e7c69bbf51c5177a20cfc5593ebd1ac766.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1002111"> <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/PMC3136429" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Sequence deeper without sequencing more: Bayesian resolution of ambiguously mapped reads

Rohan N. Shah, Alexander J. Ruthenburg, Ilya Ioshikhes
<span title="2021-04-19">2021</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
Apart from whole-genome sequencing, an NGS workflow involves alignment of the sequencing reads to the genome of study, after which the resulting alignments can be used for downstream analyses.  ...  However, alignment is complicated by the repetitive sequences; many reads align to more than one genomic locus, with 15–30% of the genome not being uniquely mappable by short-read NGS.  ...  In particular, we thank the lab of Thomas Gingeras at Cold Spring Harbor Laboratory for generating the RNA-seq data, and we thank the lab of Michael Snyder at Stanford University for generating the ATAC-seq  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1008926">doi:10.1371/journal.pcbi.1008926</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33872311">pmid:33872311</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ce32kt3dbjhq7hv4sc57afkc7q">fatcat:ce32kt3dbjhq7hv4sc57afkc7q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210423070427/https://storage.googleapis.com/plos-corpus-prod/10.1371/journal.pcbi.1008926/1/pcbi.1008926.pdf?X-Goog-Algorithm=GOOG4-RSA-SHA256&amp;X-Goog-Credential=wombat-sa%40plos-prod.iam.gserviceaccount.com%2F20210423%2Fauto%2Fstorage%2Fgoog4_request&amp;X-Goog-Date=20210423T070426Z&amp;X-Goog-Expires=3600&amp;X-Goog-SignedHeaders=host&amp;X-Goog-Signature=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" 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/bb/66/bb6685f14264e4475ef4f852b29463bc836d45d4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1008926"> <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>

iCopyDAV: Integrated platform for copy number variations—Detection, annotation and visualization

Prashanthi Dharanipragada, Sriharsha Vogeti, Nita Parekh, Ulrich Melcher
<span title="2018-04-05">2018</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;
Parallelization of the segmentation algorithms makes the iCopyDAV platform even accessible on a desktop.  ...  Performance of iCopyDAV is evaluated on both simulated data and real data for different sequencing depths.  ...  Acknowledgments PD acknowledges University Grants Commission (UGC), India for Research assistantship.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0195334">doi:10.1371/journal.pone.0195334</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29621297">pmid:29621297</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5886540/">pmcid:PMC5886540</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zhxmoy3e3vehnfecmzfelhhaoi">fatcat:zhxmoy3e3vehnfecmzfelhhaoi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719002801/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0195334&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/c8/ba/c8ba3bf2302ee422275f29a07c4eba63aa67075b.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.0195334"> <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/PMC5886540" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A randomized approach to speed up the analysis of large-scale read-count data in the application of CNV detection

WeiBo Wang, Wei Sun, Wei Wang, Jin Szatkiewicz
<span title="2018-03-01">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
The application of high-throughput sequencing in a broad range of quantitative genomic assays (e.g., DNA-seq, ChIP-seq) has created a high demand for the analysis of large-scale read-count data.  ...  Background High-throughput sequencing (HTS) has been used in a range of genomic assays in order to quantify the amount of DNA molecules (DNA-seq), or genomic regions enriched for certain biological processes  ...  The randomized algorithm is asymptotically faster than existing deterministic algorithms and is faster in numerical implementation in terms of clock time [23, 24] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-018-2077-6">doi:10.1186/s12859-018-2077-6</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29490610">pmid:29490610</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5831535/">pmcid:PMC5831535</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rwqza26sjrbbrblpg2744fcfoa">fatcat:rwqza26sjrbbrblpg2744fcfoa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430050046/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2077-6" 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/29/13/29134de0f1b6d5ede9fa36e3e509677483b5ae68.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-018-2077-6"> <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/PMC5831535" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Mapping Billions of Short Reads to a Reference Genome

Jui-Hung Hung, Zhiping Weng
<span title="2016-08-29">2016</span> <i title="Cold Spring Harbor Laboratory"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kkiieryxvje2diqdkb2ax2yiem" style="color: black;">Cold Spring Harbor Protocols</a> </i> &nbsp;
FACTORS THAT INFLUENCE MAPPABILITY The percentage of reads that map uniquely to the genome is often taken as a major result of an alignment algorithm.  ...  The algorithms search for mismatches in the query sequence at positions of high likelihood of sequencing error so that a match in the genome can be located.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/pdb.top093153">doi:10.1101/pdb.top093153</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27574203">pmid:27574203</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ce62fskuy5aqtb2tlkypnhfrnu">fatcat:ce62fskuy5aqtb2tlkypnhfrnu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180721161407/http://cshprotocols.cshlp.org/content/2017/1/pdb.top093153.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/d8/93/d8932e249df81a23ee63473d9b96ed78004cd7ae.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/pdb.top093153"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Tools and best practices for retrotransposon analysis using high-throughput sequencing data

Aurélie Teissandier, Nicolas Servant, Emmanuel Barillot, Deborah Bourc'his
<span title="2019-12-29">2019</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qmvydih3mvcjfjdugfmy26l4ee" style="color: black;">Mobile DNA</a> </i> &nbsp;
One of the biggest technical challenges with sequencing data is to map millions of reads to a reference genome.  ...  Sequencing technologies give access to a precise picture of the molecular mechanisms acting upon genome regulation.  ...  Funding The laboratory of D.B. is part of the Laboratoire d'Excellence (LABEX) entitled DEEP . This research was supported by the ERC (grant ERC-Cog EpiREPRO).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13100-019-0192-1">doi:10.1186/s13100-019-0192-1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31890048">pmid:31890048</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6935493/">pmcid:PMC6935493</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sddojvjdfjccpn32jdbzbwsdju">fatcat:sddojvjdfjccpn32jdbzbwsdju</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200326230047/https://link.springer.com/content/pdf/10.1186/s13100-019-0192-1.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/b7/d7/b7d78e9593dcbca47137a3701c6c50e4c29dfe49.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13100-019-0192-1"> <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/PMC6935493" 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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