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Graph theoretical Strategies in De Novo Assembling

Kimia Behizadi, Nafiseh Jafarzadeh, Ali Iranmanesh
2022 IEEE Access  
In this review paper, we have provided an overview of the graph-theoretical side of de novo genome assembly algorithms.  ...  INDEX TERMS Combinatorial data structures, de-Bruijn graph, de novo assembly algorithms, high throughput sequencing, overlap graph.  ...  The de-Bruijn graph algorithm for de novo assembly was originally proposed in 1995 [10] and the first DBG assembler was proposed in 2001 [11] .  ... 
doi:10.1109/access.2022.3144113 fatcat:iajrk3fq6jhbfel7apoowu3v2m

A Computer Simulator for Assessing Different Challenges and Strategies of de Novo Sequence Assembly

Bjarne Knudsen, Roald Forsberg, Michael M. Miyamoto
2010 Genes  
This study presents a new computer program for assessing the effects of different factors and sequencing strategies on de novo sequence assembly.  ...  We illustrate the application and utility of our new simulation tools with several experiments that test the effects of genome complexity (repeats), read length and coverage, word size in De Bruijn graph  ...  In terms of de novo assembly, repeats are simply sequences that occur more than once in the genome.  ... 
doi:10.3390/genes1020263 pmid:24710045 pmcid:PMC3954094 fatcat:vrhkjv76wzgqtox6cjygvnvave

The Theory and Practice of Genome Sequence Assembly

Jared T. Simpson, Mihai Pop
2015 Annual review of genomics and human genetics (Print)  
Here, we survey the key developments in algorithms for assembling genome sequences since the development of the first DNA sequencing methods more than 35 years ago. 153 Annu. Rev. Genom. Hum.  ...  sophisticated computational tools called genome assemblers (short for genome sequence assemblers).  ...  The de Bruijn graph method of sequence assembly has its roots in theoretical work from the late 1980s.  ... 
doi:10.1146/annurev-genom-090314-050032 pmid:25939056 fatcat:iayzwkwyljey5nn6hyxhwgsg7u

Integrated de novo Gene Prediction and Peptide Assembly of Metagenomic Sequencing Data [article]

Sirisha Thippabhotla, Ben Liu, Shibu Yooseph, Youngik Yang, Jun Zhang, Cuncong Zhong
2021 bioRxiv   pre-print
There are currently three main approaches for recovering novel genes or proteins: de novo nucleotide assembly, gene calling, and peptide assembly.  ...  three novel modules: a hybrid assembly graph generation module, a graph-based gene calling module, and a peptide assembly-based refinement module. iMPP significantly improved the existing gene calling  ...  Performance Metrics We benchmarked iMPP in terms of both de novo gene calling and peptide assembly. For gene calling, we compared iMPP with three other strategies.  ... 
doi:10.1101/2021.09.20.461079 fatcat:we5x74a3jbdnhkqcxj3trlsgfe

DTA-SiST: de novo transcriptome assembly by using simplified suffix trees

Jin Zhao, Haodi Feng, Daming Zhu, Chi Zhang, Ying Xu
2019 BMC Bioinformatics  
We implemented the above two strategies and compared them with the state-of-the-art de novo assemblers on both simulated and real datasets.  ...  However, the massive size of short reads makes de novo transcripts assembly an algorithmic challenge.  ...  In this situation, de novo transcriptome assembly is required. In this paper, we mainly consider de novo transcriptome assembly methods.  ... 
doi:10.1186/s12859-019-3272-9 pmid:31874618 pmcid:PMC6929406 fatcat:ah3u3zbocnbijn2lhnfiipdezi

Comparison of De Novo Transcriptome Assemblers and k-mer Strategies Using the Killifish, Fundulus heteroclitus

Satshil B. Rana, Frank J. Zadlock, Ziping Zhang, Wyatt R. Murphy, Carolyn S. Bentivegna, Wayne Iwan Lee Davies
2016 PLoS ONE  
De novo assembly of non-model organism's transcriptomes has recently been on the rise in concert with the number of de novo transcriptome assembly software programs.  ...  Comparison of De Novo Transcriptome Assemblers and k-mer Strategies PLOS ONE |  ...  Keith Cooper and Dan Milemann at Rutgers University, for their technical support in capturing and housing the killfish. Author Contributions  ... 
doi:10.1371/journal.pone.0153104 pmid:27054874 pmcid:PMC4824410 fatcat:p3iillg5vna45b3tsajnrhctjy

Assembly, Assessment, and Availability of De novo Generated Eukaryotic Transcriptomes

Joanna Moreton, Abril Izquierdo, Richard D. Emes
2016 Frontiers in Genetics  
De novo assembly in theory allows the building of a complete transcriptome without any prior knowledge of the genome.  ...  De novo assembly of a complete transcriptome without the need for a guiding reference genome is attractive, particularly where the cost and complexity of generating a eukaryote genome is prohibitive.  ...  ACKNOWLEDGMENTS AI was supported by an international PhD studentship from Consejo Nacional de Ciencia y Tecnologia (CONACYT) Mexico. JM and RE were funded by the University of Nottingham.  ... 
doi:10.3389/fgene.2015.00361 pmid:26793234 pmcid:PMC4707302 fatcat:gsg2xaznqvhnzdzzzdfrfxahl4

Next generation shotgun sequencing and the challenges of de novo genome assembly

Stephen Schlebusch, Nicola Illing
2012 South African Journal of Science  
Primers that are complementary to these regions, and which are attached to the platform, are denoted in the cognate colour with spots.  ...  There are several factors which need to be taken into consideration when planning a strategy to assemble genome sequence data de novo.  ...  This method is called a paired-end read and can be used to partially compensate for the short read lengths in de novo assembly.  ... 
doi:10.4102/sajs.v108i11/12.1256 fatcat:jpxjp5k7qnabjok7nro2btnbnq

De novo assembly of human genomes with massively parallel short read sequencing

R. Li, H. Zhu, J. Ruan, W. Qian, X. Fang, Z. Shi, Y. Li, S. Li, G. Shan, K. Kristiansen, S. Li, H. Yang (+2 others)
2009 Genome Research  
Repeat characteristics in different genomes can vary extensively, so the expected theoretical de novo assembly results from different genomes will also vary.  ...  As was shown in Figure 1B and Table 1 , the length of pairedend insert sizes determined the scaffold size of de novo genome assembly.  ... 
doi:10.1101/gr.097261.109 pmid:20019144 pmcid:PMC2813482 fatcat:mbzeuk2tcnd27fdmjbp7rpagle

IsoTree: A New Framework for De novo Transcriptome Assembly from RNA-seq Reads

Jin Zhao, Haodi Feng, Daming Zhu, Chi Zhang, Ying Xu
2018 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
Unlike most of de novo assembly methods that build de Bruijn graph or splicing graph by connecting k-mers which are sets of overlapping substrings generated from reads, IsoTree constructs splicing graph  ...  Index Terms-RNA-seq, de novo assembly, alternative splicing, transcriptome.  ...  In these situations, de novo assembly is required. In theory, a de novo assembler can reconstruct transcripts even on regions that are missing a reference.  ... 
doi:10.1109/tcbb.2018.2808350 pmid:29994455 fatcat:x6bsq7rkavftrlztlwg5ucqwiu

GAGE: A critical evaluation of genome assemblies and assembly algorithms

S. L. Salzberg, A. M. Phillippy, A. Zimin, D. Puiu, T. Magoc, S. Koren, T. J. Treangen, M. C. Schatz, A. L. Delcher, M. Roberts, G. Marcais, M. Pop (+1 others)
2012 Genome Research  
structures Efficient de novo assembly of large genomes using compressed data References Article cited in:  ...  Repeat characteristics in different genomes can vary extensively, so the expected theoretical de novo assembly results from different genomes will also vary.  ...  As was shown in Figure 1B and Table 1 , the length of pairedend insert sizes determined the scaffold size of de novo genome assembly.  ... 
doi:10.1101/gr.131383.111 pmid:22147368 pmcid:PMC3290791 fatcat:dnyq4mibszdohjvwidxp3yqgle

Transcriptome Analysis for Non-Model Organism: Current Status and Best-Practices [chapter]

Vahap Eldem, Gokmen Zararsiz, Tunahan Taşçi, Izzet Parug Duru, Yakup Bakir, Melike Erkan
2017 Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health  
In this chapter, we aim to provide an overview of the state-of-the-art methods including (i) quality check and pre-processing of raw reads, (ii) the pros and cons of de novo transcriptome assemblers, (  ...  For non-model organism, as distinct from the reference genome-based mapping, sequence reads are processed via de novo transcriptome assembly approaches to produce large numbers of contigs corresponding  ...  The sequence read length is shown to be one of the key parameters in determining de novo assembly strategy.  ... 
doi:10.5772/intechopen.68983 fatcat:vatg4hbanrchxhuxbf3meb3hye

TransComb: genome-guided transcriptome assembly via combing junctions in splicing graphs

Juntao Liu, Ting Yu, Tao Jiang, Guojun Li
2016 Genome Biology  
We present TransComb, a genome-guided assembler developed based on a junction graph, weighted by a bin-packing strategy and pairedend information.  ...  Tested on both simulated and real datasets, TransComb demonstrates significant improvements in both recall and precision over leading assemblers, including StringTie, Cufflinks, Bayesembler, and Traph.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.1186/s13059-016-1074-1 pmid:27760567 pmcid:PMC5069867 fatcat:z65fwokmtrfj7plneo7hv55cum

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

H. Li
2012 Bioinformatics  
Results: To explore the feasibility of using de novo assembly in the context of resequencing, we developed a de novo assembler, fermi, that assembles Illumina short reads into unitigs while preserving  ...  Motivation: Eugene Myers in his string graph paper (Myers, 2005) suggested that in a string graph or equivalently a unitig graph, any path spells a valid assembly.  ...  Funding: NIH Joint SNP and CNV calling in 1000 Genomes sequence data grant (1U01HG005208-01). Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/bts280 pmid:22569178 pmcid:PMC3389770 fatcat:52tfcpeuqzgspeg4tgfcqe5lhi

De novo assembly of short sequence reads

K. Paszkiewicz, D. J. Studholme
2010 Briefings in Bioinformatics  
De novo assembly of sequence reads generated by classical Sanger capillary sequencing is a mature field of research.  ...  of 30^50 nucleotides in length.  ...  Acknowledgements We are grateful to Anirvan Sengupta for making the SOPRA assembler available to us prior to publication.  ... 
doi:10.1093/bib/bbq020 pmid:20724458 fatcat:jiuokxrzs5fclfjmnpspmfr73e
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