A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies

Zhang, Wenyu; Chen, Jiajia; Yang, Yang; Tang, Yifei; Shang, Jing; Shen, Bairong

doi:10.1371/journal.pone.0017915

Cited by 212 publications

(164 citation statements)

References 32 publications

(51 reference statements)

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“…For example, measuring assemblies using simulated reads from a number of sequences including two human chromosomes, they indicate that SOAPdenovo achieved a better N50 than ABySS whereas ABySS excelled on accuracy. The study also points out that assembly quality is sensitive to the number of base-call errors only when the coverage is low (i.e., before the coverage is so high that increasing it further does not significantly increase assembly quality) [57,58].…”

Section: Assessing Performancementioning

confidence: 90%

Next-Generation Sequencing and Large Genome Assemblies

2012

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The next-generation sequencing (NGS) revolution has drastically reduced time and cost requirements for sequencing of large genomes, and also qualitatively changed the problem of assembly. This article reviews the state of the art in de novo genome assembly, paying particular attention to mammalian-sized genomes. The strengths and weaknesses of the main sequencing platforms are highlighted, leading to a discussion of assembly and the new challenges associated with NGS data. Current approaches to assembly are outlined and the various software packages available are introduced and compared. The question of whether quality assemblies can be produced using short-read NGS data alone, or whether it must be combined with more expensive sequencing techniques, is considered. Prospects for future assemblers and tests of assembly performance are also discussed. Keywordsde novo assembly; genomics; next-generation sequencing; whole-genome shotgun Genome assembly continues to be one of the central problems of bioinformatics. This is owing, in large part, to the continuing development of the sequencing technology that provides 'reads' of short sequences of DNA, from which the genome is inferred. Larger sets of data, and changes in the properties of reads such as length and errors, bring with them new challenges for assembly. For the earliest sequencing efforts using the whole-genome shotgun (WGS) approach, in which reads are generated from random locations across the entire genome, assembly could be dealt with by arranging print-outs of the reads by hand. Through the next three decades, Sanger capillary sequencing gained substantially in throughput, and WGS became practical for increasingly large and complex genomes, from tens of kilobases in the early 1980s to gigabases by 2001 [1]. In line with this, assembly went on to use not only increasingly powerful computational means, but also increasingly time and memory-efficient assemblers.A further revolution in sequencing began around 2005, when second-generation sequencing (SGS) technologies began to produce massive throughput at far lower costs than Sanger sequencing, enabling a mammalian genome to be sequenced in a matter of days [2]. De novo assemblies of the Panda [3] and Turkey [4] genomes have now been made using SGS data alone, and several human resequencing projects have been completed [5][6][7]. The © The Wellcome Trust Sanger Institute * Author for correspondence: Tel.: +44 1223 494705, Fax: +44 1223 494919, zn1@sanger.ac.uk. Financial & competing interests disclosureThe authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript. Assembly is not at all a trivial task. Repeated sequences of DNA make it difficult to infer the relative positions in the genome corresponding to reads, and they occur far more often...

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Section: Assessing Performancementioning

confidence: 90%

Next-Generation Sequencing and Large Genome Assemblies

2012

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“…To assemble new genomes, benchmark assembled reference genomes in other species are used. These include "de novo assembly algorithms" which are based on graph theory such as the de Bruijn graph formulation [28]. …”

Section: Soap3mentioning

confidence: 99%

Biomarker discovery, high performance and cloud computing: A comprehensive review

Blayney

Haberland

Lightbody

et al. 2015

2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

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Abstract-The analysis of biological markers (biomarkers) have the ability to improve clinical outcomes of a disease through prediction and early detection. The constant improvement of next generation sequencing (NGS) technologies coupled with falling equipment price are driving research and application especially in the medical domain. NGS technology is being applied to cancer research promising greater understanding of carcinogenesis. However, as sequence capacity grows, algorithmic speed is becoming an important bottleneck. To understand these challenges we present a review on difficulties currently faced in discovering biomarkers. The review places the spotlight on sequencing technologies and the bottlenecks encountered in these pipelines. Cloud computing and high performance computing technologies such as Grid are summarized in tackling computational challenges presented by technologies and algorithms used in biomarker research.

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“…Pyrosequencing (i.e. 454) data can be assembled using the GS Data Analysis Software package (http://www.454.com/products/analysis-software/), but the best program for de novo assembly of Illumina data is debated (for detailed discussion of assemblers see (Paszkiewicz & Studholme, 2010;W. Zhang, et al, 2011)).…”

Section: Bioinformatic Analysis Of Symbiont Genomes From Facs and Mdamentioning

confidence: 99%

Coupling FACS and Genomic Methods for the Characterization of Uncultivated Symbionts

Thompson

Bench

Carter

et al. 2013

Methods in Enzymology

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Symbioses between microbes are likely widespread and functionally relevant in diverse biological systems however they are difficult to discover. Most microbes remain uncultivated, symbioses can be relatively rare or dynamic, and intercellular connections can be delicate. Thus traditional methods such as microscopy are inadequate for efficient discovery and precise characterization of novel interactions, their metabolic basis, and the species involved. Highthroughput metagenomic sequencing of entire microbial communities has revolutionized the field of microbial ecology, however genomic signals from symbionts can get buried in sequences from abundant organisms and evidence for direct links between microbial species cannot be gained from bulk samples. Thus, a specialized approach to the characterization of symbioses between naturally-occurring microbes is required. This chapter presents methods for combining fluorescence-activated cell sorting (FACS) to isolate and separate uncultivated symbionts with molecular biology techniques for DNA amplification in order to characterize uncultivated symbionts through genomic and metagenomic techniques.

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A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies

Cited by 212 publications

References 32 publications

Next-Generation Sequencing and Large Genome Assemblies

Next-Generation Sequencing and Large Genome Assemblies

Biomarker discovery, high performance and cloud computing: A comprehensive review

Coupling FACS and Genomic Methods for the Characterization of Uncultivated Symbionts

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