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De novo repeat classification and fragment assembly

Pavel A. Pevzner, Haixu Tang, Glenn Tesler
2004 Proceedings of the eighth annual international conference on Computational molecular biology - RECOMB '04  
We propose a new approach to repeat classification that represents all repeats in a genome as a mosaic of sub-repeats.  ...  Our key algorithmic idea also leads to new approaches to multiple alignment and fragment assembly.  ...  ACKNOWLEDGMENTS We are indebted to Derrek Kisman, Ming Li, and Bin Ma, who kindly modified their PatternHunter software for our purposes, and to Shiaw-Pyng Yang for providing a sample of "difficult-toassemble  ... 
doi:10.1145/974614.974643 dblp:conf/recomb/PevznerTT04 fatcat:wfgtq6ypinf6npzynot7lzc464

A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data

Despoina D. Roumpeka, R. John Wallace, Frank Escalettes, Ian Fotheringham, Mick Watson
2017 Frontiers in Genetics  
De novo assembly software tools use one of two main paradigms: OLC or the de Bruijn graph approach. Both algorithms are based on graphs consisted of nodes connected with edges.  ...  Many more recent de novo assemblers use the de Bruijn graph approach (Pevzner et al., 2001) which constructs a graph by reading the consecutive kmers (sequences of k bases long) within each read.  ... 
doi:10.3389/fgene.2017.00023 pmid:28321234 pmcid:PMC5337752 fatcat:gp3iw2qoeve7bgwam7eqbln36e

GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly

Daniel L. Cameron, Jan Schröder, Jocelyn Sietsma Penington, Hongdo Do, Ramyar Molania, Alexander Dobrovic, Terence P. Speed, Anthony T. Papenfuss
2017 Genome Research  
Although our approach results in a graph two orders of magnitude larger than the equivalent de novo assembly de Bruijn graph, we are able to perform genome-wide break-end assembly faster than a number  ...  This allows us to perform genome-wide assembly without targeting or windowing and use a k-mer size half that required for de novo de Bruijn graph assembly.  ...  Although an all-in-one entry point is included, each stage of the GRIDSS pipeline, including the break-end assembler, can be run as an independent program or replaced with an equivalent implementation.  ... 
doi:10.1101/gr.222109.117 pmid:29097403 pmcid:PMC5741059 fatcat:spu72ohqmvhtpaauw7lgykkfse

Challenges in the analysis of viral metagenomes

Rebecca Rose, Bede Constantinides, Avraam Tapinos, David L Robertson, Mattia Prosperi
2016 Virus Evolution  
Notable technical challenges have impeded progress; for example, fragments of viral genomes are typically orders of magnitude less abundant than those of host, bacteria, and/or other organisms in clinical  ...  There is a growing need for intuitive analytical tooling for researchers lacking specialist computing expertise and that is applicable in diverse experimental circumstances.  ...  We thank Katrina Lithgoe and two anonymous reviewers for their helpful edits and suggestions.  ... 
doi:10.1093/ve/vew022 pmid:29492275 pmcid:PMC5822887 fatcat:sx3zsuxkjnepbd5gyyh34l22hm

deGSM: memory scalable construction of large scale de Bruijn Graph [article]

Hongzhe Guo, Yilei Fu, Yan Gao, Junyi Li, Yadong Wang, Bo Liu
2018 bioRxiv   pre-print
With the rapid development of HTS data and ever-increasing number of assembled genomes, there is a high demand to construct de Bruijn graph for sequences up to Tera-base-pair level.  ...  Motivation: De Bruijn graph, a fundamental data structure to represent and organize genome sequence, plays important roles in various kinds of sequence analysis tasks such as de novo assembly, high-throughput  ...  ., 2012) used minimizer during de Bruijn graph construction to partition de Bruijn graph into slices. This helps to reduce the memory footprint of de novo assembly.  ... 
doi:10.1101/388454 fatcat:c7sielg7vzdvxo4ppucg5akhgq

A novel codon-based de Bruijn graph algorithm for gene construction from unassembled transcriptomes

Gongxin Peng, Peifeng Ji, Fangqing Zhao
2016 Genome Biology  
We present inGAP-CDG, which can construct full-length and non-redundant coding sequences from unassembled transcriptomes by using a codon-based de Bruijn graph to simplify the assembly process and a machine  ...  Such methods are of limited application due to high transcript fragmentation and extensive assembly errors, which may lead to redundant or false coding sequence predictions.  ...  The main advantage of inGAP-CDG is that it combines a newly developed codon-based de Bruijn graph to simplify the assembly process and a machine learning based approach to filter false positives.  ... 
doi:10.1186/s13059-016-1094-x pmid:27855707 pmcid:PMC5114782 fatcat:qizttvavv5fevjuy4k2q4ch3ay

Synteny Paths for Assembly Graphs Comparison

Evgeny Polevikov, Mikhail Kolmogorov, Michael Wagner
2019 Workshop on Algorithms in Bioinformatics  
To facilitate the development of new graph-based approaches, it is important to develop algorithms for comparison and evaluation of assembly graphs produced by different software.  ...  We describe Asgan -an algorithm for efficient synteny paths decomposition, and use it to evaluate assembly graphs of various bacterial assemblies produced by different approaches.  ...  The authors have shown that incorporating the connectivity information from de Bruijn graphs improves the accuracy of metagenomic sample classification, comparing to the read mapping approaches.  ... 
doi:10.4230/lipics.wabi.2019.24 dblp:conf/wabi/PolevikovK19 fatcat:ctblipz65jcphf4tvt62xqgm3q

GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly [article]

Daniel L Cameron, Jan Schroeder, Jocelyn Sietsma Penington, Hongdo Do, Ramyar Molania, Alexander Dobrovic, Terence P Speed, Anthony Troy Papenfuss
2017 bioRxiv   pre-print
using a novel positional de Bruijn graph assembler.  ...  The identification of genomic rearrangements, particularly in cancers, with high sensitivity and specificity using massively parallel sequencing remains a major challenge.  ...  We thank Alan Rubin for helpful discussion on algorithm design. DISCLOSURE DECLARATION The authors declare that they have no competing interests.  ... 
doi:10.1101/110387 fatcat:aguiqme6orel5dwtjyq63s62m4

Next Generation Sequencing in Aquatic Models [chapter]

Yuan Lu, Yingjia Shen, Wesley Warren, Ronald Walter
2016 Next Generation Sequencing - Advances, Applications and Challenges  
Additionally, the problems that were confronted in genome sequencing of several fish models and alternative approaches to assemble these genomes will be discussed.  ...  Lastly, the problems that remain to be the bottleneck of genome sequencing will be discussed, and a plan of what needs to be fulfilled is proposed.  ...  De Bruijn graph-based assembler begins the assembling process by breaking the sequencing reads into k-mers, which in a genome is defined as a sequence of k consecutive bases.  ... 
doi:10.5772/61657 fatcat:rkmpd23h2vgsfmeawzylc7ku5u

Exploring genome characteristics and sequence quality without a reference

Jared T. Simpson
2014 Computer applications in the biosciences : CABIOS  
Motivation: The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology.  ...  Results: This article addresses the practical aspects of de novo assembly by introducing new ways to perform quality assessment on a collection of sequence reads.  ...  The project was motivated in part by online discussion of the Assemblathon2 paper centered on a blog post by Titus Brown.  ... 
doi:10.1093/bioinformatics/btu023 pmid:24443382 pmcid:PMC3998141 fatcat:4hsqdzplqbbk3dpxt75oc74esq

Information Theoretic Metagenome Assembly Allows the Discovery of Disease Biomarkers in Human Microbiome

O. Ufuk Nalbantoglu
2021 Entropy  
The current convention mainly depends on unsupervised assembly of metagenomic contigs with a possibility of leaving interesting genetic material unassembled.  ...  Our algorithm infers fragments populating the most informative genetic variants in a single contig, named supervariant fragments.  ...  Second approach involved de novo assembly and annotation of the metagenome sets.  ... 
doi:10.3390/e23020187 pmid:33540903 pmcid:PMC7913240 fatcat:uhmiwk3mwbhnnfo3vsjjjfnzdu

Exploring Genome Characteristics and Sequence Quality Without a Reference [article]

Jared T. Simpson
2013 arXiv   pre-print
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology.  ...  This paper addresses the practical aspects of de novo assembly by introducing new ways to perform quality assessment on a collection of DNA sequence reads.  ...  Leopold Parts, Zamin Iqbal and Shaun Jackman provided valuable comments on a draft of the manuscript. The use of the oyster data was suggested by Manoj Samanta.  ... 
arXiv:1307.8026v1 fatcat:qbxjpi42d5ezldwzviqzzrii6m

Ariadne: Barcoded Linked-Read Deconvolution Using de Bruijn Graphs [article]

Lauren Mak, Dmitry Meleshko, David C Danko, Waris N Barakzai, Natan Belchikov, Iman Hajirasouliha
2021 bioRxiv   pre-print
De novo assemblies are critical for capturing the genetic composition of complex samples.  ...  Integrating barcode deconvolution tools, such as Ariadne, into the postprocessing pipeline for linked-read technologies increases the quality of de novo assembly for complex populations, such as microbiomes  ...  Acknowledgements We would like to thank Indira Wu and Tuval Ben-Yehezkel at Loop Genomics for providing the MOCK5 LoopSeq dataset, as well as Yu Xia and Tom Chen at Universal Sequencing for providing the  ... 
doi:10.1101/2021.05.09.443255 fatcat:oti5sp5jf5hejf22u35hpzspqa

Misassembly Detection using Paired-End Sequence Reads and Optical Mapping Data [article]

Martin D. Muggli, Simon J. Puglisi, Roy Ronen, Christina Boucher
2014 arXiv   pre-print
A crucial problem in genome assembly is the discovery and correction of misassembly errors in draft genomes.  ...  of extensively misassembled contigs and between 57% and 73% of locally misassembed contigs in the assemblies of loblolly pine.  ...  Acknowledgements The authors would like to thank Pavel Pevzner from the University of California, San Diego and Anton Korobeynikov from Saint Petersburg State University for many insightful discussions  ... 
arXiv:1411.5890v1 fatcat:kga34kbw3jc57earmqokgunrli

Assembly of Long Error-Prone Reads Using de Bruijn Graphs [article]

Yu Lin, Jeffrey Yuan, Mikhail Kolmogorov, Max W. Shen, Pavel A. Pevzner
2016 bioRxiv   pre-print
strengths of the alternative de Bruijn graph approach to genome assembly.  ...  Moreover, these studies often assume that applications of the de Bruijn graph approach are limited to short and accurate reads and that the overlap-layout-consensus approach is the only practical paradigm  ...  Acknowledgments We are grateful to Mark Chaisson for his help with the PBcR and Quiver analysis as well as to Bahar Behsaz, Anton Korobeinikov, Mihai Pop, and Glenn Tesler for their many useful comments  ... 
doi:10.1101/048413 fatcat:uu54m5dihrbhzcftxxjuawo6ha
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