Piggy: a rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria

AbstractDespite overwhelming evidence that variation in intergenic regions (IGRs) in bacteria impacts on phenotypes, most current approaches for analysing pan-genomes focus exclusively on protein-coding sequences. To address this we present Piggy, a novel pipeline that emulates Roary except that it is based only on IGRs. We demonstrate the use of Piggy for pan-genome analyses of Staphylococcus aureus and Escherichia coli using large genome datasets. For S. aureus, we show that highly divergent (“switched”) IGRs are associated with differences in gene expression, and we establish a multi-locus reference database of IGR alleles (igMLST; implemented in BIGSdb). Piggy is available at https://github.com/harry-thorpe/piggy.

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Roary: Rapid large-scale prokaryote pan genome analysis

10.1101/019315 ◽

2015 ◽

Cited By ~ 9

Author(s):

Andrew J Page ◽

Carla A Cummins ◽

Martin Hunt ◽

Vanessa K Wong ◽

Sandra Reuter ◽

...

Keyword(s):

Genetic Structure ◽

Genome Analysis ◽

Large Scale ◽

The Core ◽

Pan Genome ◽

Accessory Genes ◽

Multiple Processors ◽

Prokaryotic Genomes ◽

Accuracy Of Results

A typical prokaryote population sequencing study can now consist of hundreds or thousands of isolates. Interrogating these datasets can provide detailed insights into the genetic structure of of prokaryotic genomes. We introduce Roary, a tool that rapidly builds large-scale pan genomes, identifying the core and dispensable accessory genes. Roary makes construction of the pan genome of thousands of prokaryote samples possible on a standard desktop without compromising on the accuracy of results. Using a single CPU Roary can produce a pan genome consisting of 1000 isolates in 4.5 hours using 13 GB of RAM, with further speedups possible using multiple processors.

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Critical assessment of pan-genomics of metagenome-assembled genomes

10.1101/2022.01.13.476228 ◽

2022 ◽

Author(s):

Tang Li ◽

Yanbin Yin

Keyword(s):

Genome Analysis ◽

Phylogenetic Trees ◽

Large Scale ◽

Gene Loss ◽

Core Gene ◽

Critical Assessment ◽

Major Influence ◽

The Core ◽

Pan Genome ◽

Analysis Tools

Background: Large scale metagenome assembly and binning to generate metagenome-assembled genomes (MAGs) has become possible in the past five years. As a result, millions of MAGs have been produced and increasingly included in pan-genomics workflow. However, pan-genome analyses of MAGs may suffer from the known issues with MAGs: fragmentation, incompleteness, and contamination, due to mis-assembly and mis-binning. Here, we conducted a critical assessment of including MAGs in pan-genome analysis, by comparing pan-genome analysis results of complete bacterial genomes and simulated MAGs. Results: We found that incompleteness led to more significant core gene loss than fragmentation. Contamination had little effect on core genome size but had major influence on accessory genomes. The core gene loss remained when using different pan-genome analysis tools and when using a mixture of MAGs and complete genomes. Importantly, the core gene loss was partially alleviated by lowering the core gene threshold and using gene prediction algorithms that consider fragmented genes, but to a less degree when incompleteness was higher than 5%. The core gene loss also led to incorrect pan-genome functional predictions and inaccurate phylogenetic trees. Conclusions: We conclude that lowering core gene threshold and predicting genes in metagenome mode (as Anvio does with Prodigal) are necessary in pan-genome analysis of MAGs to alleviate the accuracy loss. Better quality control of MAGs and development of new pan-genome analysis tools specifically designed for MAGs are needed in future studies.

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Roary: rapid large-scale prokaryote pan genome analysis

Bioinformatics ◽

10.1093/bioinformatics/btv421 ◽

2015 ◽

Vol 31 (22) ◽

pp. 3691-3693 ◽

Cited By ~ 1325

Author(s):

Andrew J. Page ◽

Carla A. Cummins ◽

Martin Hunt ◽

Vanessa K. Wong ◽

Sandra Reuter ◽

...

Keyword(s):

Genome Analysis ◽

Large Scale ◽

Pan Genome

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Faculty Opinions recommendation of Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.732499418.793559379 ◽

2019 ◽

Author(s):

Laura Privalle

Keyword(s):

Genome Analysis ◽

Wild Rice ◽

Genomic Variation ◽

Pan Genome

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PRISMS-Fatigue computational framework for fatigue analysis in polycrystalline metals and alloys

npj Computational Materials ◽

10.1038/s41524-021-00506-8 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Mohammadreza Yaghoobi ◽

Krzysztof S. Stopka ◽

Aaditya Lakshmanan ◽

Veera Sundararaghavan ◽

John E. Allison ◽

...

Keyword(s):

Open Source ◽

Open Source Software ◽

Large Scale ◽

Metals And Alloys ◽

Analysis Tool ◽

Computational Framework ◽

Crystal Plasticity Finite Element ◽

Polycrystalline Metals ◽

Simulation Based ◽

Open Source Framework

AbstractThe PRISMS-Fatigue open-source framework for simulation-based analysis of microstructural influences on fatigue resistance for polycrystalline metals and alloys is presented here. The framework uses the crystal plasticity finite element method as its microstructure analysis tool and provides a highly efficient, scalable, flexible, and easy-to-use ICME community platform. The PRISMS-Fatigue framework is linked to different open-source software to instantiate microstructures, compute the material response, and assess fatigue indicator parameters. The performance of PRISMS-Fatigue is benchmarked against a similar framework implemented using ABAQUS. Results indicate that the multilevel parallelism scheme of PRISMS-Fatigue is more efficient and scalable than ABAQUS for large-scale fatigue simulations. The performance and flexibility of this framework is demonstrated with various examples that assess the driving force for fatigue crack formation of microstructures with different crystallographic textures, grain morphologies, and grain numbers, and under different multiaxial strain states, strain magnitudes, and boundary conditions.

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Characterization of Pharmaceutical Tablets Using UV Hyperspectral Imaging as a Rapid Line to Line Analysis Tool

Sensors ◽

10.3390/s21134436 ◽

2021 ◽

Vol 21 (13) ◽

pp. 4436

Author(s):

Mohammad Al Ktash ◽

Mona Stefanakis ◽

Barbara Boldrini ◽

Edwin Ostertag ◽

Marc Brecht

Keyword(s):

Hyperspectral Imaging ◽

Large Scale ◽

Solid Phase ◽

Ultra Violet ◽

Principal Component ◽

Ccd Camera ◽

Conveyor Belt ◽

Hyperspectral Data ◽

Analysis Tool ◽

Sample Set

A laboratory prototype for hyperspectral imaging in ultra-violet (UV) region from 225 to 400 nm was developed and used to rapidly characterize active pharmaceutical ingredients (API) in tablets. The APIs are ibuprofen (IBU), acetylsalicylic acid (ASA) and paracetamol (PAR). Two sample sets were used for a comparison purpose. Sample set one comprises tablets of 100% API and sample set two consists of commercially available painkiller tablets. Reference measurements were performed on the pure APIs in liquid solutions (transmission) and in solid phase (reflection) using a commercial UV spectrometer. The spectroscopic part of the prototype is based on a pushbroom imager that contains a spectrograph and charge-coupled device (CCD) camera. The tablets were scanned on a conveyor belt that is positioned inside a tunnel made of polytetrafluoroethylene (PTFE) in order to increase the homogeneity of illumination at the sample position. Principal component analysis (PCA) was used to differentiate the hyperspectral data of the drug samples. The first two PCs are sufficient to completely separate all samples. The rugged design of the prototype opens new possibilities for further development of this technique towards real large-scale application.

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SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes

PLoS Computational Biology ◽

10.1371/journal.pcbi.1008439 ◽

2020 ◽

Vol 16 (12) ◽

pp. e1008439

Author(s):

Jennifer Lu ◽

Steven L. Salzberg

Keyword(s):

Large Scale ◽

Analysis Tool ◽

Index Test ◽

Bacterial Genomes ◽

Phylogenetic Groups ◽

Bacterial Phyla ◽

Link Type ◽

Gc Skew ◽

A Genome ◽

Web App

GC skew is a phenomenon observed in many bacterial genomes, wherein the two replication strands of the same chromosome contain different proportions of guanine and cytosine nucleotides. Here we demonstrate that this phenomenon, which was first discovered in the mid-1990s, can be used today as an analysis tool for the 15,000+ complete bacterial genomes in NCBI’s Refseq library. In order to analyze all 15,000+ genomes, we introduce a new method, SkewIT (Skew Index Test), that calculates a single metric representing the degree of GC skew for a genome. Using this metric, we demonstrate how GC skew patterns are conserved within certain bacterial phyla, e.g. Firmicutes, but show different patterns in other phylogenetic groups such as Actinobacteria. We also discovered that outlier values of SkewIT highlight potential bacterial mis-assemblies. Using our newly defined metric, we identify multiple mis-assembled chromosomal sequences in previously published complete bacterial genomes. We provide a SkewIT web app https://jenniferlu717.shinyapps.io/SkewIT/ that calculates SkewI for any user-provided bacterial sequence. The web app also provides an interactive interface for the data generated in this paper, allowing users to further investigate the SkewI values and thresholds of the Refseq-97 complete bacterial genomes. Individual scripts for analysis of bacterial genomes are provided in the following repository: https://github.com/jenniferlu717/SkewIT.

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Pan-Genome Analysis of Mycobacterium Africanum: Insights to Dynamics and Evolution.

10.21203/rs.3.rs-34142/v1 ◽

2020 ◽

Author(s):

Idowu Olawoye ◽

Simon D.W. Frost ◽

Christian T. Happi

Keyword(s):

West Africa ◽

Genome Analysis ◽

West African ◽

Multiple Copy ◽

Genome Sequences ◽

Animal Reservoir ◽

Pan Genome ◽

Lineage Specificity ◽

Mycobacterium Africanum ◽

Core Genes

Abstract Background: Mycobacterium tuberculosis complex (MTBC) consists of seven major lineages with three of them reported to circulate within West Africa: lineage 5 (West African 1) and lineage 6 (West African 2) which are geographically restricted to West Africa and lineage 4 (Euro-American lineage) which is found globally. It is unclear why the West African lineages are not found elsewhere; some hypotheses suggest that it could either be harboured by an animal reservoir which is restricted to West Africa, or strain preference for hosts of West African ethnicity, or inability to compete with other lineages in other locations.We tested the hypothesis that M. africanum West African 2 (lineage 6) might have emigrated out of West Africa but was outcompeted by more virulent modern strains of M. tuberculosis (MTB).Whole genome sequences of M. tuberculosis from Nigeria (n=21), South Africa (n=24) and M. africanum West African 2 from Mali (n=22) were retrieved, and a pan-genome analysis was performed after fully annotating these genomes. Results: The outcome of this analysis shows that Lineages 2, 4 and 6 all have a close pan-genome. We also see a correlation in numbers of some multiple copy core genes and amino acid substitution with lineage specificity that may have contributed to geographical distribution of these lineages.Conclusions: The findings in this study provides a perspective to one of the hypotheses that M. africanum West African 2 might find it difficult to compete against the more modern lineages outside West Africa hence its localization to the geographical region.

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Signifikansi Pengaruh Sentimen Pemberlakuan PSBB Terhadap Aspek Ekonomi: Pengaruh Pada Nilai Tukar Rupiah dan Stock Return (Studi Kasus Pandemi Covid-19)

Jurnal Bina Akuntansi ◽

10.52859/jba.v7i2.98 ◽

2020 ◽

Vol 7 (2) ◽

pp. 223-239

Author(s):

Irma Lestari Made

Keyword(s):

Exchange Rate ◽

Stock Returns ◽

Stock Return ◽

Large Scale ◽

Herd Immunity ◽

Wilcoxon Test ◽

Analysis Tool ◽

Public Sentiment ◽

Before And After ◽

The Government

The Large-Scale Social Limitation Policy (Pembatasan Sosial Berskala Besar/PSBB) was chosen by the Indonesian government in responding to the pandemic covid-19. The PSBB policy is preferred by the government to be implemented instead of lockdown. Much controversy in public over the PSBB policy has built the sentiment. Consideration of the economic aspects has been the main reason in making these policies. With consideration of the state of the Indonesian economy, the government believes that this policy is an effective and efficient pathway with a note that the public will be able to conduct pandemic covid-19 health protocol discipline and form herd immunity. This study aims to evaluate the effect of the implementation of the PSBB which has an impact on public sentiment fluctuations, using secondary stock return data on blue-chip stocks and the rupiah exchange rate in the range of time before and after the implementation of the PSBB begun, April 10, 2020. Wilcoxon test is used as data analysis tool of nonparametric statistics. The test results stated that the exchange rate of the rupiah against the US dollar was significantly affected by public sentiment towards the implementation of the PSBB, while the stock return was not significantly affected. Several factors beyond the implementation of PSBB need to be considered in influencing stock returns as well as the rupiah exchange rate.

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