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Graph theoretical Strategies in De Novo Assembling
2022
IEEE Access
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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
2010
Genes
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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
2015
Annual review of genomics and human genetics (Print)
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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]
2021
bioRxiv
pre-print
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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
2019
BMC Bioinformatics
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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
2016
PLoS ONE
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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
2016
Frontiers in Genetics
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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
2012
South African Journal of Science
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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
2009
Genome Research
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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
2018
IEEE/ACM Transactions on Computational Biology & Bioinformatics
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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
2012
Genome Research
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structures Efficient de novo assembly of large genomes using compressed data References http://genome.cshlp.org/content/20/2/265.full.html#related-urls Article cited in: http://genome.cshlp.org/content ...
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]
2017
Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health
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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
2016
Genome Biology
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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
2012
Bioinformatics
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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
2010
Briefings in Bioinformatics
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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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