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Read Mapping Algorithms for Single Molecule Sequencing Data [chapter]

Vladimir Yanovsky, Stephen M. Rumble, Michael Brudno
Lecture Notes in Computer Science  
In this paper we develop novel rapid alignment algorithms for two-pass Single Molecule Sequencing methods.  ...  Single Molecule Sequencing technologies such as the Heliscope simplify the preparation of DNA for sequencing, while sampling millions of reads in a day.  ...  alignment algorithm for next-generation Single Molecule Sequencing (SMS) platforms.  ... 
doi:10.1007/978-3-540-87361-7_4 fatcat:cpzdh7xtzzckta2ivlcaprp6me

HapIso : An Accurate Method for the Haplotype-Specific Isoforms Reconstruction from Long Single-Molecule Reads [article]

Serghei Mangul, Harry Taegyun Yang, Farhad Hormozdiari, Elizabeth Tseng, Alex Zelikovsky, Eleazar Eskin
2016 bioRxiv   pre-print
Single-molecule protocols generate multi-kilobase reads longer than most transcripts allowing sequencing of complete haplotype isoforms.  ...  Furthermore, our method is the first method able to reconstruct the haplotype-specific isoforms from long single-molecule reads.  ...  (A) The algorithm takes long single-molecule reads that have been mapped to the reference genome as an input.  ... 
doi:10.1101/050906 fatcat:tt4pr75x4zgtzlnr3ckgetouca

Structural Variation Detection from Next Generation Sequencing

Ye K, Hall G
2015 Journal of Next Generation Sequencing & Applications  
At the end, we highlight the impact and potential applications of the 3rd generation sequencing data, generated from PacBio and Oxford Nanopore long read sequencing platforms.  ...  In this short review, we mainly discuss various algorithms and computational tools for identifying SVs of different types and sizes with a brief introduction to complex SVs.  ...  Single Molecule Real Time sequencing (SMRT) from PacBio is a parallelized single molecule DNA sequencing method.  ... 
doi:10.4172/2469-9853.s1-007 fatcat:k3vahmfg3bbkxj53fyg24ch6ci

VALOR2: characterization of large-scale structural variants using linked-reads

Fatih Karaoğlanoğlu, Camir Ricketts, Ezgi Ebren, Marzieh Eslami Rasekh, Iman Hajirasouliha, Can Alkan
2020 Genome Biology  
Here, we propose novel algorithms to characterize large interspersed segmental duplications, inversions, deletions, and translocations using linked-read sequencing data.  ...  We redesign our earlier algorithm, VALOR, and implement our new algorithms in a new software package, called VALOR2.  ...  Meleshko for the computational support. We also thank M. Chaisson for early access to the HGSV data. Review history The review history is available as Additional file 2.  ... 
doi:10.1186/s13059-020-01975-8 pmid:32192518 fatcat:mgb64nuyfngoxapoowihm66ru4

Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore technologies reveals platform-specific error patterns

Alla Mikheenko, Andrey D Prjibelski, Anoushka Joglekar, Hagen U Tilgner
2022 biorxiv/medrxiv  
We summarize these findings in an annotation-based algorithm for spliced alignment correction that improves subsequent transcript construction with ONT reads.  ...  Our single-molecule technology comparison reveals that inconsistencies are often caused by sequencing-error induced inaccurate ONT alignments, especially to downstream GUNNGU donor motifs.  ...  Acknowledgments We thank Alyona Sidorova and Alexandra Bazarova for their aid with the analysis. This work was supported by NIGMS (grant 1R01GM135247-01 to H.U.T), St.  ... 
doi:10.1101/gr.276405.121 pmid:35301264 pmcid:PMC8997348 fatcat:gouenqjoqjfyfea6fiodeh76ie

leeHom: adaptor trimming and merging for Illumina sequencing reads

Gabriel Renaud, Udo Stenzel, Janet Kelso
2014 Nucleic Acids Research  
Our algorithm is faster, and provides a more accurate reconstruction of the original sequence for both simulated and ancient DNA data sets, than other approaches. leeHom is released under the GPLv3 and  ...  The sequencing of libraries containing molecules shorter than the read length, such as in ancient or forensic applications, may result in the production of reads that include the adaptor, and in paired  ...  ACKNOWLEDGEMENT We thank Kay Prüfer for useful comments and Amin Saffari for testing the software.  ... 
doi:10.1093/nar/gku699 pmid:25100869 pmcid:PMC4191382 fatcat:qppxzzgmcndnpfenuhfrg2kasq

Advances in optical mapping for genomic research

Yuxuan Yuan, Claire Yik-Lok Chung, Ting-Fung Chan
2020 Computational and Structural Biotechnology Journal  
Here, we review the development of optical mapping in recent decades to illustrate its importance in genomic research. We detail its applications and algorithms to show its specific advantages.  ...  Optical mapping also enables genome comparison and identification of large-scale structural variations.  ...  The concept of de novo single-molecule map assembly is similar to that of assembly in sequence contexts.  ... 
doi:10.1016/j.csbj.2020.07.018 pmid:32802277 pmcid:PMC7419273 fatcat:j7pbytromndbnbr6vxp7vjzvqq

Mapping Billions of Short Reads to a Reference Genome

Jui-Hung Hung, Zhiping Weng
2016 Cold Spring Harbor Protocols  
The output of a mapping algorithm becomes the input data for subsequent analysis.  ...  Lengths of DNA molecules being sequenced compared with size of reference genome. For some experiments, the DNA molecules being sequenced may be shorter than the read length of the sequencer.  ... 
doi:10.1101/pdb.top093153 pmid:27574203 fatcat:ce62fskuy5aqtb2tlkypnhfrnu

Hybrid error correction and de novo assembly of single-molecule sequencing reads

Sergey Koren, Michael C Schatz, Brian P Walenz, Jeffrey Martin, Jason T Howard, Ganeshkumar Ganapathy, Zhong Wang, David A Rasko, W Richard McCombie, Erich D Jarvis, Adam M Phillippy
2012 Nature Biotechnology  
To address this limitation, we introduce a correction algorithm and assembly strategy that uses short, highfidelity sequences to correct the error in single-molecule sequences.  ...  Single-molecule sequencing instruments can generate multikilobase sequences with the potential to greatly improve genome and transcriptome assembly.  ...  Potential improvements to the PBcR algorithm include the addition of a gap-closure routine to fill sequencing gaps in the short-read data using the PacBio reads and incorporation of the single-molecule  ... 
doi:10.1038/nbt.2280 pmid:22750884 pmcid:PMC3707490 fatcat:wiou4fgizjdobow5mbedgzyqm4

Whole-genome haplotyping approaches and genomic medicine

Gustavo Glusman, Hannah C Cox, Jared C Roach
2014 Genome Medicine  
The main approaches for phasing genomic sequence data are molecular haplotyping, genetic haplotyping, and population-based inference.  ...  Current technologies generate diploid sequence data that is rarely resolved into its constituent haplotypes.  ...  GG and JCR received support from and the National Institute of General Medical Sciences Center for Systems Biology (P50 GM076547). We thank the anonymous reviewers for their contributions.  ... 
doi:10.1186/s13073-014-0073-7 pmid:25473435 pmcid:PMC4254418 fatcat:3cwkvkr4k5bfba3cobsey4mphq

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

Qiong-Yi Zhao, Jacob Gratten, Restuadi Restuadi, Xuan Li
2016 Quantitative Biology  
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.  ...  In this review, we discuss recent developments in RNA-Seq data analysis applied to model organisms, including methods and algorithms for direct mapping, reference-guided transcriptome assembly and differential  ...  Jennifer Whitehead for critical reading of the manuscript. This work is supported by the National Health and Medical Research Council project grants (Nos.  ... 
doi:10.1007/s40484-016-0060-7 fatcat:idomdo4pdjgr3o7jvz44w2uxlu

Characterization of structural variants with single molecule and hybrid sequencing approaches

Anna Ritz, Ali Bashir, Suzanne Sindi, David Hsu, Iman Hajirasouliha, Benjamin J. Raphael
2014 Computer applications in the biosciences : CABIOS  
Results: We present MultiBreak-SV, an algorithm to detect structural variants from single molecule sequencing data, paired read sequencing data, or a combination of sequencing data from different platforms  ...  Recent "third-generation" sequencing technologies provide single-molecule templates and longer sequencing reads, but at the cost of higher per-nucleotide error rates.  ...  Acknowledgments: We thank Mark Chaisson at PacBio for his insight with running and tuning BLASR for long read alignments in the early stage of this work.  ... 
doi:10.1093/bioinformatics/btu714 pmid:25355789 pmcid:PMC4253835 fatcat:c6ezqojyqbbcnei3hmmfl5dkom

De novo sequencing and variant calling with nanopores using PoreSeq

Tamas Szalay, Jene A Golovchenko
2015 Nature Biotechnology  
class of 6 algorithm can reliably surpass the accuracy of single molecule reads (Fig. 1b) when the 7 implementation is tailored appropriately to the task of nanopore sequencing. 8 The base-calling algorithm  ...  modified single-23 molecule Viterbi algorithm that deliberately introduces some randomness (Supplementary Note 24 2).  ...  a single nanopore sequencing read. 2D Viterbi Algorithm.  ... 
doi:10.1038/nbt.3360 pmid:26352647 pmcid:PMC4877053 fatcat:xip7mre4lnf7dd2at3ksxfw42i

Biochemical and bioinformatic methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation

A. Kloetgen, P. C. Munch, A. Borkhardt, J. I. Hoell, A. C. McHardy
2014 Briefings in Functional Genomics  
In combination with immunoprecipitation and deep sequencing techniques, tens of millions of short reads (representing bound RNAs by an RBP of interest) are generated and are used to characterize the regulatory  ...  In this review, we discuss experimental and computational methods for the generation and analysis of CLIP data.The computational methods include short-read alignment, annotation and RNA-binding motif discovery  ...  Acknowledgements The authors acknowledge Christina Kratsch for her previous work on our in-house pipeline for the analysis of NGS and PAR-CLIP data.  ... 
doi:10.1093/bfgp/elu020 pmid:24951655 pmcid:PMC4471435 fatcat:6dmi7a6os5ajloprdk4hdz42wi

Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools

Janna L. Fierst
2015 Frontiers in Genetics  
Genetic linkage maps based on recombination rates between physical markers 5 have been used in biology for over 100 years and a linkage map, when paired with a de novo 6 sequencing project, can resolve  ...  mis-assemblies and anchor chromosome-scale sequences. 7 Here, I summarize the methodology behind integrating de novo assemblies and genetic linkage 8 maps, outline the current challenges, review the available  ...  Pacific Biosciences single molecule real time (SMRT) 87 sequencing (Eid et al., 2008) produces reads with a median length of 3,122bp but the per-base accuracy is 88 87% (Koren et al., 2013).  ... 
doi:10.3389/fgene.2015.00220 pmid:26150829 pmcid:PMC4473057 fatcat:f5kf2ht4mjdsfg6rcltdvqfhti
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