C-Sibelia: an easy-to-use and highly accurate tool for bacterial genome comparison

Minkin, Ilya; Pham, Hoa; Starostina, Ekaterina; Vyahhi, Nikolay; Pham, Son

doi:10.12688/f1000research.2-258.v1

Cited by 31 publications

(25 citation statements)

References 10 publications

(13 reference statements)

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“…The complete genome was annotated by Prokka 18 , version 1.14.5, software. The mutations were analyzed with the use of Sibelia 19 , version 3.07, software, based on existing Wuhan-Hu-1 (NC_045512.2) genome and were annotated by SnpEff 20 , version 4.3, software. We integrated information from 60 published genomic sequences of SARS-CoV-2.…”

Section: Whole-genome Sequencing and Comparative Genome Analysismentioning

confidence: 99%

Nosocomial outbreak of COVID-19 pneumonia in Wuhan, China

et al. 2020

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BackgroundThe novel coronavirus (SARS-CoV-2) infected over 3,300 health-care-workers (HCWs) in early 2020 in China. Little information is known about nosocomial infections of HCWs in the initial period. We analyzed data from HCWs with nosocomial infections in Wuhan Union Hospital and their family members. MethodsWe collected and analyzed data on exposure history, illness timelines, and epidemiologic characteristics of 25 laboratory-confirmed and two highly suspected HCWs as well as ten of their family members with COVID-19 from Jan 5 to Feb 12, 2020. Among them, demographics and clinical features of the 35 laboratory-confirmed cases were investigated and viral RNA of 12 cases was sequenced and analyzed. ResultsNine clusters were found among the patients. All patients showed mild to moderate clinical manifestation and recovered without deterioration. The average periods of incubation, clinical onset serial interval (COSI), and virus shedding were 4.5 days, 5.2 ± 3.2 days, and 18.5 days, respectively. Complete genomic sequences of 12 different coronavirus strains demonstrated that the viral structure with small, irrelevant mutations was stable in the transmission chains and showed remarkable traits of infectious traceability. ConclusionsSARS-CoV-2 can be rapidly transmitted person-to-person regardless of whether they have symptoms in both hospital settings and social activities based on the short period of incubation and COSI. The public health service should take practical measures to curb the spread, including isolation of cases, tracing close-contacts, and containment of severe epidemic areas. Besides, the HCWs should be alert during the epidemic, and make self-quarantine if self-suspected. Nosocomial Outbreak of 2019 Novel

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Section: Whole-genome Sequencing and Comparative Genome Analysismentioning

confidence: 99%

Nosocomial outbreak of COVID-19 pneumonia in Wuhan, China

et al. 2020

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“…The contigs were aligned and ordered against M. tuberculosis H37Rv using Mauve v.2.3.1 (8). Synteny evaluation and visualization were carried out using C-Sibelia (9) and Circos (10). The genome of M. tuberculosis MTB-476 consists of 257 contigs with a G+C content of 65.2% and 4,204 predicted coding sequences, 46 tRNAs, and 3 rRNAs.…”

Section: Genome Announcementmentioning

confidence: 99%

Draft Genome Sequences of Two Clinical Isolates of Mycobacterium tuberculosis from Sputum of Kazakh Patients

et al. 2015

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“…These are blocks that are free from non-linear rearrangements, such as inversions or transpositions. Once such blocks are identified, they can independently be globally aligned (Darling et al, 2004;Dewey, 2007;Paten et al, 2008;Darling et al, 2010;Minkin et al, 2013a). Such strategies are generally better at scaling to handle repeats and multiple genomes since they do not rely on the computationally expensive pairwise alignment.…”

Section: Introductionmentioning

confidence: 99%

“…This allows it to maintain a simple, static, data structure, which scales easily and allows simple parallelization. Thus, SibeliaZ-LCB overcomes a bottleneck of previous state-of-the-art de Bruijn graph-based approaches Minkin et al, 2013a), which relied on a dynamic data structure which was expensive to update. Further, we extend SibeliaZ-LCB into a multiple whole-genome aligner called SibeliaZ.…”

Section: Introductionmentioning

confidence: 99%

Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ

Minkin

Medvedev

2019

Preprint

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Multiple whole-genome alignment is a fundamental and challenging problems in bioinformatics. Despite many ongoing successes, today's methods are not able to keep up with the growing number, length, and complexity of assembled genomes. Approaches based on using compacted de Bruijn graphs to identify and extend anchors into locally collinear blocks hold the potential for scalability, but current algorithms still do not scale to mammalian genomes. We present a novel algorithm SibeliaZ-LCB for identifying collinear blocks in closely related genomes based on the analysis of the de Bruijn graph. We further incorporate it into a multiple whole-genome alignment pipeline called SibeliaZ. SibeliaZ shows drastic run-time improvements over other methods on both simulated and real data, with only a limited decrease in accuracy. On sixteen recently assembled strains of mice, SibeliaZ runs in under 12 hours, while other tools could not run to completion for even eight mice, given a week. SibeliaZ makes a significant step towards improving scalability of multiple whole-genome alignment and collinear block reconstruction algorithms and will enable many comparative genomics studies in the near future.

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C-Sibelia: an easy-to-use and highly accurate tool for bacterial genome comparison

Cited by 31 publications

References 10 publications

Nosocomial outbreak of COVID-19 pneumonia in Wuhan, China

Nosocomial outbreak of COVID-19 pneumonia in Wuhan, China

Draft Genome Sequences of Two Clinical Isolates of Mycobacterium tuberculosis from Sputum of Kazakh Patients

Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ

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