Long walk to genomics: History and current approaches to genome sequencing and assembly

Giani, Alice Maria; Gallo, Guido Roberto; Gianfranceschi, L.; Formenti, Giulio

doi:10.1016/j.csbj.2019.11.002

Cited by 217 publications

(150 citation statements)

References 183 publications

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“…In the last five years, novel WGS strategies based on single molecule, long-read sequencing technologies have been successful in improving the quality of the nuclear genome assemblies, particularly in repetitive regions 32 . Since single-molecule DNA sequencing can currently produce reads of at least 10-20 kbp in size 32 , a complete full-length representation of mtDNA genomes can theoretically be obtained in a single read, solving the overlap uncertainty issue of short-read NGS and Sanger-based approaches. However, since single molecule sequencing technologies have a relatively high error rate, assembly is still required to derive an accurate consensus sequence.…”

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confidence: 99%

Complete vertebrate mitogenomes reveal widespread gene duplications and repeats

Formenti

Rhie

Balacco

et al. 2020

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AbstractModern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. As part of the Vertebrate Genomes Project (VGP) we have developed mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (>10 kbp, PacBio or Nanopore) and short (100-300 bp, Illumina) reads. Our pipeline led to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We have observed that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we have identified errors, missing sequences, and incomplete genes in those references, particularly in repeat regions. Our assemblies have also identified novel gene region duplications, shedding new light on mitochondrial genome evolution and organization.

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confidence: 99%

Complete vertebrate mitogenomes reveal widespread gene duplications and repeats

Formenti

Rhie

Balacco

et al. 2020

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“…Remarkable progress has been made to advance genome assemblies in recent decades, including cost-efficient and accurate high-throughput short-read sequencing, long-read single molecule sequencing, and improved assembly and error correction algorithms (34,35). The evaluation of multiple versions of assemblies using different assembly algorithms and various assembly procedures is critical for optimization of genome assemblies.…”

Section: Discussionmentioning

confidence: 99%

Estimating Assembly Base Errors Using K-mer Abundance Difference (KAD) Between Short Reads and Genome Assembled Sequences

Lin

et al. 2020

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Genome sequences provide genomic maps with a single-base resolution for exploring genetic contents. Sequencing technologies, particularly long reads, have revolutionized genome assemblies for producing highly continuous genome sequences. However, current long-read sequencing technologies generate inaccurate reads that contain many errors. Some errors are retained in assembled sequences, which are typically not completely corrected by using either long reads or more accurate short reads. The issue commonly exists but few tools are dedicated for computing error rates or determining error locations. In this study, we developed a novel approach, referred to as K-mer Abundance Difference (KAD), to compare the inferred copy number of each k-mer indicated by short reads and the observed copy number in the assembly. Simple KAD metrics enable to classify k-mers into categories that reflect the quality of the assembly. Specifically, the KAD method can be used to identify base errors and estimate the overall error rate. In addition, sequence insertion and deletion as well as sequence redundancy can also be detected. Therefore, KAD is valuable for quality evaluation of genome assemblies and, potentially, provides a diagnostic tool to aid in precise error correction. KAD software has been developed to facilitate public uses.

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“…age, specimen source and status), gender served as a compulsory criterion for profiling the excavated genomes. Male isolates excavated according to Country (number of sequence, state(s) extracted), include: Algeria (2, 1); Benin (5, 2); Cameroon (1, 1); DRC (15,4); Egypt (5, 2); Gambia (6, 2); Ghana (4, 1); Kenya (4, 1); Mali (5, 2); Morocco (5, 3); Nigeria (13,5); Senegal (14,6); South Africa (65,20); Tunisia (1, 1). Female isolates excavated according to country (number of sequence, state(s) extracted), include: Algeria (1, 1); Benin (4, 1); DRC (13,4); Egypt (4, 2); Gambia (4, 2); Ghana (4, 1); Kenya (4, 1); Madagascar (2, 2); Mali (4, 1); Morocco (2, 1); Nigeria (11,5); Senegal (11,3); South Africa (80, 24); Tunisia (1, 1).…”

Section: Data Source and Genome Sequences Selectionmentioning

confidence: 99%

Real Time Viral Sub-Strains Discovery in Emerging Infectious Disease Situation – The African Perspective

Ekpenyong¹,

Uzoka²,

Edoho³

et al. 2020

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BackgroundThe increased number of accessible genomes has prompted large-scale comparative studies for decerning evolutionary knowledge of infectious diseases, but challenges such as non-availability of close reference sequence(s), incompletely assembled or large number of genomes, preclude real time multiple sequence alignment and sub-strain(s) discovery. This paper introduces a cooperatively inspired open-source framework, for intelligent mining of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genomes. We situate this study within the African context, to drive advancement on state-of-the-art, towards intelligent infectious disease characterization and prediction. The outcome is an enriched Knowledge Base, sufficient to provide deep understanding of the viral sub-strains’ identification problem. We also open investigation by gender, which to the best of our knowledge has been ignored in related research. Data for the study came from the Global Initiative on Sharing All Influenza Data database (https://gisaid.org) and processed for precise discovery of viral sub-strains transmission between and within African countries. To localize the transmission route(s) of each isolate excavated and provide appropriate links to similar isolate strain(s), a cognitive solution was imposed on the genome expression patterns discovered by unsupervised self-organizing map (SOM) component planes visualization. The Freidman-Nemenyi’s test was finally performed to validate our claim.ResultsEvidence of inter- and intra-genome diversity was noticed. While some isolates (or genomes) clustered differently, implying different evolutionary source (or high-diversity), others clustered closely together, indicating similar evolutionary source (or less-diversity). SOM component planes analysis revealed multiple sub-strains patterns, strongly suggesting local or intra-community and country to country transmissions. Cognitive maps of both male and female isolates revealed multiple transmission routes. Statistical results indicate significant difference between the various isolate groups at the 0.05 level of significance.ConclusionThe proposed framework offers explanations to SARS-CoV-2 diversity and provides real time identification to disease transmission routes, as well as rapid decision support for facilitating inter- and intra-country contact tracing of infected case(s). Intermediate data produced in this paper are helpful to enrich the genome datasets for intelligent characterization and prediction of COVID-19 and related pandemics, as well as the construction of intelligent device for accurate infectious disease monitoring.

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Long walk to genomics: History and current approaches to genome sequencing and assembly

Abstract: Graphical abstract

Cited by 217 publications

References 183 publications

Complete vertebrate mitogenomes reveal widespread gene duplications and repeats

Complete vertebrate mitogenomes reveal widespread gene duplications and repeats

Estimating Assembly Base Errors Using K-mer Abundance Difference (KAD) Between Short Reads and Genome Assembled Sequences

Real Time Viral Sub-Strains Discovery in Emerging Infectious Disease Situation – The African Perspective

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