Choice of assemblers has a critical impact on de novo assembly of SARS-CoV-2 genome and characterizing variants

Islam, Rizwanul; Raju, Rajan Saha; Tasnim, Nazia; Shihab, Istiak Hossain; Bhuiyan, Maruf Ahmed; Araf, Yusha; Islam, Tofazzal

doi:10.1093/bib/bbab102

Cited by 13 publications

(9 citation statements)

References 29 publications

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“…The choice of assembler is significant too. MEGAHIT normally outperforms other assemblers in speed [ 29 ]. Natively, Captus can handle the tasks following user-specified arguments of threads and parallelization, which is not the case for HybPiper and SECAPR.…”

Section: Discussionmentioning

confidence: 99%

Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines

Raza,

Ortiz,

Schwung

et al. 2023

BMC Ecol Evo

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Background Despite recent advances, reliable tools to simultaneously handle different types of sequencing data (e.g., target capture, genome skimming) for phylogenomics are still scarce. Here, we evaluate the performance of the recently developed pipeline Captus in comparison with the well-known target capture pipelines HybPiper and SECAPR. As test data, we analyzed newly generated sequences for the genus Thladiantha (Cucurbitaceae) for which no well-resolved phylogeny estimate has been available so far, as well as simulated reads derived from the genome of Arabidopsis thaliana. Results Our pipeline comparisons are based on (1) the time needed for data assembly and locus extraction, (2) locus recovery per sample, (3) the number of informative sites in nucleotide alignments, and (4) the topology of the nuclear and plastid phylogenies. Additionally, the simulated reads derived from the genome of Arabidopsis thaliana were used to evaluate the accuracy and completeness of the recovered loci. In terms of computation time, locus recovery per sample, and informative sites, Captus outperforms HybPiper and SECAPR. The resulting topologies of Captus and SECAPR are identical for coalescent trees but differ when trees are inferred from concatenated alignments. The HybPiper phylogeny is similar to Captus in both methods. The nuclear genes recover a deep split of Thladiantha in two clades, but this is not supported by the plastid data. Conclusions Captus is the best choice among the three pipelines in terms of computation time and locus recovery. Even though there is no significant topological difference between the Thladiantha species trees produced by the three pipelines, Captus yields a higher number of gene trees in agreement with the topology of the species tree (i.e., fewer genes in conflict with the species tree topology).

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Section: Discussionmentioning

confidence: 99%

Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines

Raza,

Ortiz,

Schwung

et al. 2023

BMC Ecol Evo

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“…A previous study reported the effects of different genome assemblies built from the same data on gene annotation and SNP annotations, which showed the importance of a high-quality genome assembly and consensus in the data inputs for downstream analysis (Florea et al, 2011). Another study on acute respiratory syndrome coronavirus 2 (SARS-CoV-2) also indicated that the choice of assemblers plays a significant role in the detection of variants and a number of variants present in assemblies are unique to the assembly methods (Islam et al, 2021). Hence, as sequencing methods are diversifying and increasingly new assembly algorithms are being developed, future genome downstream analysis such as detection of SVs should take the same data input into consideration to eliminate differences resulting from the data and assembly methods.…”

Section: Discussionmentioning

confidence: 99%

Extensive sequence divergence between the reference genomes of two zebrafish strains, Tuebingen and AB

Deng

Qian

Meng³

et al. 2022

Molecular Ecology Resources

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The zebrafish (Danio rerio) is one of the most widely used model organisms for studying vertebrate gene function and human disease, given the 70% conserved proteincoding genes between zebrafish and human. Two of the most common laboratory zebrafish strains are Tuebingen and AB. Despite the fact that the zebrafish reference genome is derived from the Tuebingen strain, the AB strain is still widely used although a high-quality genome comparable to Tuebingen is lacking. Here, we report a 1.40-Gb representative de novo genome assembly of the AB strain (DrAB1), with contig N50 length of 21 Mb, by integrating Illumina short-read sequencing, Nanopore long-read sequencing and HiC-based chromatin mapping. Compared with the published zebrafish Zv11 reference genome (GRCz11), this genome assembly shows considerable improvements in both contiguity and completeness. In addition, substantial structural differences and extensive sequence divergence of unprecedented resolution have been uncovered, especially with respect to 9,029,929 single nucleotide polymorphisms, 2,376,812 InDels, 32,623 insertions, 22,089 deletions and 220 inversions, which constitute ~2.6% of the DrAB1 genome. Many of these variants may have potential functional effects on phenotype, which should be considered in further experimental designs. Consequently, our study provides additional genomic resources and a high-resolution structural variation map based on whole-genome alignment for the zebrafish community, which could also be an indispensable reference genome from a model species in future research on fish phylogenetic genomics, comparative genomics and adaptive evolution.

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“…where π(•) is a row vector and ∑ π(•) = 1. We explore how many mutation steps will converge by computing the information entropy H(x) with Equations ( 8) and (9).…”

Section: Proof Of Convergence Interval Of the Mutation Simulation Modelmentioning

confidence: 99%

“…In terms of SARS-CoV-2 intra-host mutation spectra computation, although recent studies already analyzed the intra-host mutation spectra of SARS-CoV-2 [7,8], they neither employed dynamics thresholds to filter low-quality data during raw sequencing data processing nor considered data specificity. Furthermore, since most of these computational methods are based on next-generation sequencing data, which is inherently deficient in short read-length and the need of amplification, thus it is difficult to accurately distinguish positive-and negative-sense sub-genomes or to further investigate the strand specificity of SARS-CoV-2 intra-host mutants [5,9]. Therefore, our first scientific question is how to develop such a data specificity-based base filtering algorithm for SARS-CoV-2 sequencing data that can significantly improve the accuracy of strand-specific mutation spectra computation for SARS-CoV-2.…”

Section: Introductionmentioning

confidence: 99%

A Computer Simulation of SARS-CoV-2 Mutation Spectra for Empirical Data Characterization and Analysis

Xiao

et al. 2022

Biomolecules

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It is very important to compute the mutation spectra, and simulate the intra-host mutation processes by sequencing data, which is not only for the understanding of SARS-CoV-2 genetic mechanism, but also for epidemic prediction, vaccine, and drug design. However, the current intra-host mutation analysis algorithms are not only inaccurate, but also the simulation methods are unable to quickly and precisely predict new SARS-CoV-2 variants generated from the accumulation of mutations. Therefore, this study proposes a novel accurate strand-specific SARS-CoV-2 intra-host mutation spectra computation method, develops an efficient and fast SARS-CoV-2 intra-host mutation simulation method based on mutation spectra, and establishes an online analysis and visualization platform. Our main results include: (1) There is a significant variability in the SARS-CoV-2 intra-host mutation spectra across different lineages, with the major mutations from G- > A, G- > C, G- > U on the positive-sense strand and C- > U, C- > G, C- > A on the negative-sense strand; (2) our mutation simulation reveals the simulation sequence starts to deviate from the base content percentage of Alpha-CoV/Delta-CoV after approximately 620 mutation steps; (3) 2019-NCSS provides an easy-to-use and visualized online platform for SARS-Cov-2 online analysis and mutation simulation.

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Choice of assemblers has a critical impact on de novo assembly of SARS-CoV-2 genome and characterizing variants

Cited by 13 publications

References 29 publications

Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines

Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines

Extensive sequence divergence between the reference genomes of two zebrafish strains, Tuebingen and AB

A Computer Simulation of SARS-CoV-2 Mutation Spectra for Empirical Data Characterization and Analysis

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