GAGE-B: an evaluation of genome assemblers for bacterial organisms

Magoč, Tanja; Pabinger, Stephan; Canzar, Stefan; Liu, Xinyue; Su, Qi; Puiu, Daniela; Tallon, Luke J.; Salzberg, Steven L.

doi:10.1093/bioinformatics/btt273

Cited by 143 publications

(142 citation statements)

References 25 publications

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“…Reads that could be mapped to the B. aphidicola or mitochondrial genomes were removed as their coverage levels would otherwise lead them to be retained in this read set. Only read pairs that remained intact following these filtering steps were included, and these pairs (which totaled 8.8 million read pairs) were assembled using SPAdes (Bankevich et al, 2012), which has been reported to perform well with bacterial genomes (Magoc et al, 2013). Several k-mer sizes were combined in SPAdes (31,41,63,81,89), with default values employed for the other parameters.…”

Section: De Novo Assembly and Characterization Of An Aphid Symbiont Gmentioning

confidence: 99%

Whole-genome re-sequencing of non-model organisms: lessons from unmapped reads

et al. 2014

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Unmapped reads are often discarded from the analysis of whole-genome re-sequencing, but new biological information and insights can be uncovered through their analysis. In this paper, we investigate unmapped reads from the re-sequencing data of 33 pea aphid genomes from individuals specialized on different host plants. The unmapped reads for each individual were retrieved following mapping to the Acyrthosiphon pisum reference genome and its mitochondrial and symbiont genomes. These sets of unmapped reads were then cross-compared, revealing that a significant number of these unmapped sequences were conserved across individuals. Interestingly, sequences were most commonly shared between individuals adapted to the same host plant, suggesting that these sequences may contribute to the divergence between host plant specialized biotypes. Analysis of the contigs obtained from assembling the unmapped reads pooled by biotype allowed us to recover some divergent genomic regions previously excluded from analysis and to discover putative novel sequences of A. pisum and its symbionts. In conclusion, this study emphasizes the interest of the unmapped component of re-sequencing data sets and the potential loss of important information. We here propose strategies to aid the capture and interpretation of this information. Heredity (2015) 114, 494-501; doi:10.1038/hdy.2014.85; published online 1 October 2014 INTRODUCTION Next-generation sequencing and whole-genome re-sequencing is nowadays commonly used to identify genomic variants that underlie phenotypic variations, genetic diseases, adaptation or speciation in natural populations. Typically, the reads are mapped against a reference genome, and the genotypes (that is, single-nucleotide polymorphism (SNP) and structural variant calls) are based on these mapped reads (Altshuler et al., 2010;Nielsen et al., 2011). In addition to universal caveats regarding unknown insertions and/or genomic contamination, which can be overlooked in pure mapping approaches, non-model organisms may suffer from the poor quality of the nuclear reference genome and incomplete symbiont or organellar genomes. Moreover, mapping is constrained by the level of divergence between the reads and the available reference sequence (Sousa and Hey, 2013). The resulting ascertainment bias could be problematic, especially when studying adaptation or speciation processes, as genomic regions of interest are expected to display important levels of divergence. These different issues produce a non-negligible fraction of unmapped reads, whose sequences are generally disregarded in favor of the mapped reads in the subsequent steps of the analysis, despite potentially containing useful information. This study offers one strategy for mining the unmapped reads in order to extract the relevant biological knowledge, leading to advice and recommendations for other re-sequencing projects.We investigated this question in the context of a large-scale resequencing project on the pea aphid species complex. The pea aphid

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Section: De Novo Assembly and Characterization Of An Aphid Symbiont Gmentioning

confidence: 99%

Whole-genome re-sequencing of non-model organisms: lessons from unmapped reads

et al. 2014

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“…The Genomics Standards Consortium is an open-membership group that is helping to drive standardization activities (73). The N50, which is similar to the mean of lengths but assigns more weight to larger contigs, is sometimes used to assess assembly quality (74,75). However, the practical implications of this value, such as what N50 value is required to yield an assembly with a complete gene for every gene in a core genome, have yet to be determined.…”

Section: Standards For Quality and Quantitymentioning

confidence: 99%

Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing

et al. 2016

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SUMMARYThe epidemiological investigation of a foodborne outbreak, including identification of related cases, source attribution, and development of intervention strategies, relies heavily on the ability to subtype the etiological agent at a high enough resolution to differentiate related from nonrelated cases. Historically, several different molecular subtyping methods have been used for this purpose; however, emerging techniques, such as single nucleotide polymorphism (SNP)-based techniques, that use whole-genome sequencing (WGS) offer a resolution that was previously not possible. With WGS, unlike traditional subtyping methods that lack complete information, data can be used to elucidate phylogenetic relationships and disease-causing lineages can be tracked and monitored over time. The subtyping resolution and evolutionary context provided by WGS data allow investigators to connect related illnesses that would be missed by traditional techniques. The added advantage of data generated by WGS is that these data can also be used for secondary analyses, such as virulence gene detection, antibiotic resistance gene profiling, synteny comparisons, mobile genetic element identification, and geographic attribution. In addition, several software packages are now available to generatein silicoresults for traditional molecular subtyping methods from the whole-genome sequence, allowing for efficient comparison with historical databases. Metagenomic approaches using next-generation sequencing have also been successful in the detection of nonculturable foodborne pathogens. This review addresses state-of-the-art techniques in microbial WGS and analysis and then discusses how this technology can be used to help support food safety investigations. Retrospective outbreak investigations using WGS are presented to provide organism-specific examples of the benefits, and challenges, associated with WGS in comparison to traditional molecular subtyping techniques.

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“…Contiguity and correctness are two attributes of the resultant assembly that can be assessed. There have recently been reports in the literature focused on comparing the performances of assembly workflows (8,(106)(107)(108)(109). Common summary statistics for genome assemblies include the total number and lengths of the contigs.…”

Section: De Novo Assemblymentioning

confidence: 99%

A Primer on Infectious Disease Bacterial Genomics

et al. 2016

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SUMMARYThe number of large-scale genomics projects is increasing due to the availability of affordable high-throughput sequencing (HTS) technologies. The use of HTS for bacterial infectious disease research is attractive because one whole-genome sequencing (WGS) run can replace multiple assays for bacterial typing, molecular epidemiology investigations, and more in-depth pathogenomic studies. The computational resources and bioinformatics expertise required to accommodate and analyze the large amounts of data pose new challenges for researchers embarking on genomics projects for the first time. Here, we present a comprehensive overview of a bacterial genomics projects from beginning to end, with a particular focus on the planning and computational requirements for HTS data, and provide a general understanding of the analytical concepts to develop a workflow that will meet the objectives and goals of HTS projects.

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GAGE-B: an evaluation of genome assemblers for bacterial organisms

Cited by 143 publications

References 25 publications

Whole-genome re-sequencing of non-model organisms: lessons from unmapped reads

Whole-genome re-sequencing of non-model organisms: lessons from unmapped reads

Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing

A Primer on Infectious Disease Bacterial Genomics

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