Tag: SPAdes

Contigs number vs NNN gap % in WGS

Contigs number vs NNN gap % in WGS 0 Hi all, I have two fasta files of bacterial whole genome sequence assembly (same genome) generated by spades generated by spades > extra scaffolding step using multi-csar, by comparing it to 5 close genomes. quast statistics as below : Genome 1…

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Senior Bioinformatics Scientist in Chicago, IL for University of Chicago (UC)

Details Posted: 19-Dec-23 Location: Chicago, Illinois Type: Full-time Salary: Open Categories: Research – Laboratory/Non-Laboratory Staff/Administrative Location: Chicago, IL Job Description: Development of an integrated data warehouse for symbiote including clinical, microbiome sequence, and metabolomic data.  Management of DFI Biobank, MMF, and HMMF data within the Symbiote platform. Functional analysis of…

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Senior Bioinformatics Scientist @ University of Chicago

Department BSD DFI – Translational Informatics About the Department The Duchossois Family Institute focuses on the role of commensal bacteria in enhancing disease resistance and is using genomic and metabolomic platforms to characterize the microbiome and its metabolites. Computational and bioinformatic expertise is required to understand how commensal bacteria impact…

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How to whole genome assemble when I have three references

How to whole genome assemble when I have three references 0 Hello, I am new to bioinformatics and am having trouble with an assembly. I have illumina miseq short pair-ended reads from an organism that has multiple yeast chromosomes and a single bacterial chromosome with portions of a plasmid inside….

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SPADes Tool

Forum:SPADes Tool 0 0 Entering edit mode 2 hours ago hafizshaheerahmad006 • 0 why should I chose SPADes assembler tool over the Velvet and other for MRSA genomic study Bioinformatics Assembler MRSA SPADes • 14 views ADD COMMENT • link 2 hours ago by hafizshaheerahmad006 • 0 Login before adding…

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Pair ended short reads assemble to multiple references with a plasmid also inside

Pair ended short reads assemble to multiple references with a plasmid also inside 0 Hello, I am new to bioinformatics and am having trouble doing an assembly and alignment. First I will describe my sample data, I have Illumina MiSeq data of pair ended reads on a yeast organism. This…

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Genome sequence and characterization of a novel Pseudomonas putida phage, MiCath

Bacterial strains We used P. putida strains S12, DOT-T1E, F1 (kindly gifted by Grant Rybnicky), ATCC 12633 (purchased from ATCC), JUb85 (kindly provided by Samuel Buck), EM383 (kindly gifted by Huseyin Tas), p106 (kindly provided by Carey-Ann Burnham), and KT2440 (obtained from lab stocks). An overnight culture of each P….

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The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution

FAO, ITPS, GSBI, CBD & EC. State of knowledge of soil biodiversity – Status, challenges and potentialities, Report 2020. (FAO). doi.org/10.4060/cb1928en. 2020. Potapov, A. M. et al. Feeding habits and multifunctional classification of soil-associated consumers from protists to vertebrates. Biol. Rev. 97, 1057–1117 (2022). Article  PubMed  Google Scholar  García-Palacios, P.,…

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From Metagenomics to Ecogenomics: NGS-Based Approaches for Discovery of New Circular DNA Single-Stranded Viral Species

doi: 10.1007/978-1-0716-3515-5_7. Affiliations Expand Affiliations 1 Departamento de Biotecnología Agrícola, Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Guasave, Sinaloa, Mexico. 2 Department of Plant Biochemistry, Center for Plant Molecular Biology (ZMBP), Eberhard Karls University, Tübingen, Germany. 3 Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones…

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Comparative genomics and proteomics analysis of phages infecting multi-drug resistant Escherichia coli O177 isolated from cattle faeces

Batinovic, S. et al. Bacteriophages in natural and artificial environments. Pathogens 8, 100. doi.org/10.3390/pathogens8030100 (2019). Article  PubMed  PubMed Central  Google Scholar  Mushegian, A. R. Are there 10^31 virus particles on earth, or more, or fewer?. J. Bacteriol. 202(9), 2020. doi.org/10.1128/JB.00052-20 (2020). Article  Google Scholar  Kutter, E. & Sulakvelidze, A. Bacteriophages:…

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Alfalfa vein mottling virus, a novel potyvirid infecting Medicago sativa L. | Virology Journal

Plant material Five alfalfa plants (stems and leaves) were sampled from each of the four different fields, 10–15 acres in size, located in Yuma Country, Arizona, USA. Geographic coordinates of the alfalfa fields and the adjacent crops are shown in Table 1. Table 1 Geographic locations of alfalfa fields Total…

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Using metagenome assembly and binning to identify and mitigate contamination in a genome

Hi everyone, This may be a silly question, but I am interested if using metagenome assembly and binning is a valid method of determining if a sample contains a mixture of species. Similarly, can metagenomics be used to identify and remove contamination from a single genome? For some background, I…

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unicycler error : [Errno 13] Permission denied:

I was running unicycler and encountered an error in permisson, what steps should I take to resolve this issue? [Errno 13] Permission denied: Command line: /home/default1/miniconda3/envs/unicycler/bin/spades.py -o /mnt/d/raw/2023nudi/01.RawData/De-unicycler/output3/spades_assembly -k 27 –threads 9 –isolate -1 /mnt/d/raw/2023nudi/01.RawData/De-unicycler/Nudivirus_DKDN230027457-1A_HJHVHDSX7_L1.1qc.fq -2 /mnt/d/raw/2023nudi/01.RawData/De-unicycler/Nudivirus_DKDN230027457-1A_HJHVHDSX7_L1.2qc.fq -m 1024 System information: SPAdes version: 3.15.5 Python version: 3.10.8 OS: Linux-4.4.0-19041-Microsoft-x86_64-with-glibc2.31 Output…

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finished abnormally, OS return value: 21

SPAdes error: finished abnormally, OS return value: 21 1 I’m having trouble using SPAdes. I’m using SPAdes to do paired end data assembly and I’m getting an unusual stop. error code: finished abnormally, OS return value: 21 Do you know how to resolve this issue? Environment: conda, SPAdes genome assembler…

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using RSEM with non Trinity assembly

using RSEM with non Trinity assembly 0 Hi all, I am trying to use RSEM to receive relative abundance estimates of viruses within my metagenomic data, not transcripts. The problem is that I am no longer using Trinity as the assembler because I had much better luck with SPAdes, especially…

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Construction of single sequence assembly out of contigs

Construction of single sequence assembly out of contigs 0 I have 396 contigs/scaffolds of Illumina short paired-end reads. Assembly of bacterial reads is generated through spades (de novo assembler). I have to make single sequence genome out of 396 contigs/scaffolds. I don’t have long reads. Kindly suggest any pipeline or…

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Genome mining reveals novel biosynthetic gene clusters in entomopathogenic bacteria

Katz, L. & Baltz, R. H. Natural product discovery: Past, present, and future. J. Ind. Microbiol. Biotechnol. 43, 155–176 (2016). Article  CAS  PubMed  Google Scholar  Newman, D. J. & Cragg, G. M. Natural products as sources of new drugs from 1981 to 2014. J. Nat. Prod. 79, 629–661 (2016). Article …

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Draft genome sequencing of halotolerant bacterium Salinicola sp. DM10 unravels plant growth-promoting potentials

Afridi MS, Amna S et al (2019) Induction of tolerance to salinity in wheat genotypes by plant growth promoting endophytes: Involvement of ACC deaminase and antioxidant enzymes. Plnat Physiol Biochem 139:569–577. doi.org/10.1016/j.plaphy.2019.03.041 Article  CAS  Google Scholar  Ali S, Charles TC, Glick BR (2014) Amelioration of high salinity stress damage by…

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did pilon improve my genome?

did pilon improve my genome? 0 my doubt is if my sequence has actually improved? refseq is the reference sequence. polished is the output from pilon and contigs.fasta is my file generated from spades. pls help I used the command Java -Xmx2048m -jar pilon-1.24.jar –genome refseq.fasta –frags sorted bam.bam –output…

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Genome sequence and characterization of Streptomyces phages Vanseggelen and Verabelle, representing two new species within the genus Camvirus

Bacteriophage isolation Streptomyces phages Vanseggelen and Verabelle were isolated from a soil sample obtained from the National Park Zuid-Kennemerland in the Netherlands (N52° 23′ 31″, E4° 34′ 49″) using Streptomyces coelicolor as the host. Details on isolation procedures are reported previously in detail12. The collected phage stock solutions were stored…

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Uncertainty of how to proceed with Metagenomic Analysis of WGS data

Uncertainty of how to proceed with Metagenomic Analysis of WGS data 1 Hello guys, I am relatively new to metagenomic data analysis and even bioinformatics in general. To maybe give you a brief idea of what my issue is, I will just explain what my data is about: the data…

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Characteristics of Klebsiella pneumoniae co-infections

Introduction Tuberculosis (TB), caused by Mycobacterium tuberculosis (M. tuberculosis), is a prominent issue in the field of global public health, particularly in lower-middle-income-countries. Nearly two-thirds of global TB cases come from eight countries, including China.There are 780,000 new TB cases in China every year.1 TB is characterized by increased risk…

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Spades Log not updating – ran overnight for 6 MB file, still running

Spades Log not updating – ran overnight for 6 MB file, still running 0 I am trying to run spades on a multi-fastq file of short sequences, but it seems to be stuck in one spot the whole night. This is what the spades log has been the entire night,…

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Widespread and largely unknown prophage activity, diversity, and function in two genera of wheat phyllosphere bacteria

Isolation of phyllosphere isolates All bacterial strains were isolated in June 2021 from the flag leaves of four wheat cultivars (Sheriff, Heerup, Rembrandt and Kvium) grown in an experimental field in Høje Taastrup, near Copenhagen, Denmark. Wheat flag leaves were picked, pooled, and either washed or blended prior to dilution…

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Strain-level diversity of symbiont communities between individuals and populations of a bioluminescent fish

Sachs JL, Ehinger MO, Simms EL. Origins of cheating and loss of symbiosis in wild Bradyrhizobium. J Evol Biol. 2010;23:1075-89. Carrow HC, Batachari LE, Chu H. Strain diversity in the microbiome: Lessons from Bacteroides fragilis. PLoS Pathog. 2020;16:e1009056. Article  CAS  PubMed  PubMed Central  Google Scholar  Martinez J, Tolosana I, Ok…

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N50 value of bacterial assembly is not half of total assembly size

N50 value of bacterial assembly is not half of total assembly size 0 Dear scientists, I have performed de novo assembly of bacterial WGS data using spades and abyss. However I am not sure which assembly approach is good to go because N50 value is not half or more than…

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Tools for reference-guided de novo assembly of bacterial genome

Tools for reference-guided de novo assembly of bacterial genome 1 Dear all, Please suggest which tool should i use for optimal assembly of bacterial fastq reads. Which approach is good if reference genome is available: de novo assembly or reference-guided de novo assembly? And also do spades assist with reference…

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Metagenome Assembled Genomes (MAG) Facilitate a Better Understanding of Microbially-mediated Heavy Metal Resistance in Soils from a Former Nuclear Materials Production Facility

Abstract Shotgun metagenomes is a repository of all the genes present in an environmental sample. With recent advancements in bioinformatic techniques, it is now possible to in-silico retrieve sequences that belong to specific taxa, followed by assembly and annotation and the obtained sequences are called as metagenome-assembled genome (MAG), which…

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rnaSPAdes running out of memory: oom error

rnaSPAdes running out of memory: oom error 0 I am trying to assemble a metatranscriptome sample (~83M reads) using rnaSPAdes (v 3.13.0), and I am running out of memory on these runs. After running the following code: rnaspades.py -m 1500 -t 8 -o rnaSPAdes_output_37 –pe1-1 SM037_R1.fastq –pe1-2 SM037_R2.fastq I get…

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Salmon and SPAdes contigs filtering

Salmon and SPAdes contigs filtering 0 Hello! I have a bunch of reference contigs, obtained with SPAdes, and RNA-seq data analyzed with salmon for control and experimental sample (let it be c_ and 2_). For every gene, there are several contigs, differing by length. Here are some tables Control: ~$…

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Metagenome sequencing and recovery of 444 metagenome-assembled genomes from the biofloc aquaculture system

Uncultured microorganisms constitute a significant proportion of microbial populations in an ecosystem and play a vital role in its functioning1. The challenges associated with cultivating these microbes have constrained access to the vast phylogenetic and functional diversity they possess. However, recent advancements in metagenomics have opened a new window to…

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Index of /~psgendb/birchhomedir/public_html/doc/pkg/spades/osx-x86_64/share/spades/spades_pipeline/scripts

Name Last modified Size Description Parent Directory   –   breaking_scaffolds_s..> 2019-12-26 08:20 1.8K   check_test_script.py 2021-11-29 14:45 3.6K   compress_all.py 2020-04-22 07:38 4.9K   copy_files.py 2019-12-26 08:20 820   correction_iteration..> 2020-04-22 07:38 3.3K   plasmid_glue.py 2022-01-31 17:00 1.1K   postprocessing_scrip..> 2021-11-29 14:45 3.4K   preprocess_contigs.py 2021-12-22 11:58 2.4K  …

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Distantly related Alteromonas bacteriophages share tail fibers exhibiting properties of transient chaperone caps

de Jonge, P. A., Nobrega, F. L., Brouns, S. J. J. & Dutilh, B. E. Molecular and evolutionary determinants of bacteriophage host range. Trends Microbiol. 27, 51–63 (2019). Article  PubMed  Google Scholar  Cambillau, C. Bacteriophage module reshuffling results in adaptive host range as exemplified by the baseplate model of listerial…

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Genomic Characteristics of Carbapenem-Resistant Klebsiella pneumoniae

Introduction Klebsiella pneumoniae (K. pneumoniae), which belongs to the family Enterobacteriaceae, is a common nosocomial pathogen that causes a variety of human infections, including bloodstream infection, respiratory tract infection, urinary tract infection, and abdominal infection.1,2 Carbapenems are generally considered to be a last choice for the treatment of multi-drug resistant…

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Oxygen respiration and polysaccharide degradation by a sulfate-reducing acidobacterium

Rabus, R., Hansen, T. A. & Widdel, F. In Dissimilatory Sulfate-and Sulfur-Reducing Prokaryotes. The Prokaryotes: Prokaryotic Physiology and Biochemistry, Rosenberg E., DeLong E. F., Lory S., Stackebrandt E., and Thompson F. at (2013). Rabus, R. et al. Chapter Two—A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing…

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Genomic insights into Bacillus subtilis MBB3B9 mediated aluminium stress mitigation for enhanced rice growth

Bian, M. et al. Development of gene-specific markers for acid soil/aluminium tolerance in barley (Hordeum vulgare L.). Mol. Breed. 32, 155–164 (2013). Article  CAS  Google Scholar  Kochian, L. V., Piñeros, M. A., Liu, J. & Magalhaes, J. V. Plant adaptation to acid soils: The molecular basis for crop aluminum resistance….

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Nvidia’s Remarkable Journey: From Gaming to AI Dominance | by Vic Danh | Sep, 2023

Unveiling the Evolution of Nvidia — CNBC and WSJ Insights Welcome back to our “The Economics of…” series, where we delve into the fascinating stories of companies that have left an indelible mark on the business world. In this installment, we explore Nvidia, a company that has evolved from being…

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Average Coverage after Assembly (Spades)

Average Coverage after Assembly (Spades) 1 Hi, I would like to know to average coverage of my assemblies (gotten by spades). I ran bbmap to mapping my reads (the same ones I used to make the assembly) to the assembly. But I am not really sure that is the way…

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Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis

Neilson, J. W. et al. Significant impacts of increasing aridity on the arid soil microbiome. mSystems 2, e00195–e00116 (2017). Article  CAS  PubMed  PubMed Central  Google Scholar  Fierer, N. et al. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc. Natl Acad. Sci. USA 109, 21390–21395 (2012). Article …

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Genome-Based Prediction of Bacterial Antibiotic Resistance

Abdelbary M, Basset P, Blanc D et al (2017) In: Tibayrenc M (ed) Genetics and evolution of infectious diseases: the evolution and dynamics of methicillin-resistant Staphylococcus aureus, 2nd edn. Elsevier, pp 553–572. ISBN: 9780127999425 CrossRef  Google Scholar  Allard MW, Stevens EL, Brown EW (2019) All for one and one for…

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Longitudinal genomic surveillance of carriage and transmission of Clostridioides difficile in an intensive care unit

Guh, A. Y. et al. Trends in U.S. Burden of Clostridioides difficile infection and outcomes. N. Engl. J. Med. 382, 1320–1330 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  Antibiotic Resistance Threats in the United States (Centers for Disease Control and Prevention, 2019); doi.org/10.15620/cdc:82532 Evans, C. T. & Safdar, N….

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Whole genomes from bacteria collected at diagnostic units around the world 2020

Preparation of partners to collect samples Partners registered for participation by contributing isolates or DNA samples to the study. Material was sent to partners according to their registered participation format. This included material for sample collection, metadata registration, DNA extraction and sample shipment to Denmark. Specific protocols were provided, according…

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RdRp scan – identifying/detecting viruses- metagenomic workflow

RdRp scan – identifying/detecting viruses- metagenomic workflow- need help 0 Good afternoon fellow biologists, I have just discovered the joy of bioinformatics on linux (and its frustrations). However, I don’t really understand the workflow for the RdRp scan method to detect viruses. => doi.org/10.1093/ve/veac082 => FIGURE 10 For now: I…

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The genetic variability of grapevine Pinot gris virus (GPGV) in Australia | Virology Journal

Giampetruzzi A, Roumi V, Roberto R, Malossini U, Yoshikawa N, La Notte P, et al. A new grapevine virus discovered by deep sequencing of virus-and viroid-derived small RNAs in Cv Pinot gris. Virus Res. 2012;163(1):262–8. doi.org/10.1016/j.virusres.2011.10.010. Article  CAS  PubMed  Google Scholar  Bertazzon N, Forte V, Filippin L, Causin R, Maixner…

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Why is my genome assembly not aligning well?

Why is my genome assembly not aligning well? 0 Hello, I am working on a genome assembly. I assembled the genome using SPADES. I used QUAST to assess the genome and got the result All statistics are based on contigs of size >= 500 bp, unless otherwise noted (e.g., “#…

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Solved explain these figuresSummary of the 16S and 18S

explain these figuresSummary of the 16S and 18S small-subunit (SSU) rRNA genes extracted in four different ways: three assembly sets run against HMMs {long reads assembled with metaFlye (“metaFlye + HMMs”), long and short reads assembled with hybridSPAdes (“hybridSPAdes + HMMs”), and short reads assembled with metaSPAdes [“Illumina (SPAdes +…

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Short Read Data Genome Assembly

Short Read Data Genome Assembly 1 Hello, I have recently started working on genome assembly of a fungus genome.I have illumina short read sequencing paired-end (2x150bp) data taken from NCBI. Based on this data, I am trying to set up pipeline for genome assembly, which can later be used for…

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Genomic and transcriptomic analysis of camptothecin producing novel fungal endophyte: Alternaria burnsii NCIM 1409

Atanasov, A. G. et al. Discovery and resupply of pharmacologically active plant-derived natural products: A review. Biotechnol. Adv. 33, 1582–1614 (2015). Article  CAS  PubMed  PubMed Central  Google Scholar  Swamy, M. K. et al. Biotechnology of camptothecin production in Nothapodytes nimmoniana, Ophiorrhiza sp. and Camptotheca acuminata. Appl. Microbiol. Biotechnol. 105, 9089–9102…

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Cathie Wood Loads Up on These 2 Innovation Stocks

Perceived wisdom goes that the way to outperform the market this year has been by leaning into the Magnificent Seven stocks (AAPL, AMZN, GOOGL, META, MSFT, NVDA, TSLA). These market leaders – all tech giants – are seen as being responsible for the market’s rally, but hold that thought, says…

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Differential gene expression analysis after transcriptome assembly with SPAdes

Differential gene expression analysis after transcriptome assembly with SPAdes 0 Hello.I’m was recommended to use SPAdes for transcriptome assembly. I didn’t find explanation on quantification and differential expression analysis after the assembly in the program’s documentation, Does anybody have any recommendations for proper programs? SPAdes differential-expression transcriptome-assembly • 25 views…

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Emergence of putative energy parasites within Clostridia revealed by genome analysis of a novel endosymbiotic clade

Cryan JF, O’Riordan KJ, Cowan CSM, Sandhu KV, Bastiaanssen TFS, Boehme M, et al. The microbiota-gut-brain axis. Physiol Rev. 2019;99:1877–2013. Article  CAS  PubMed  Google Scholar  Lopetuso LR, Scaldaferri F, Petito V, Gasbarrini A. Commensal clostridia: leading players in the maintenance of gut homeostasis. Gut Pathog. 2013;5:e23. Article  Google Scholar  Collins…

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Functional annotation and comparative genomics analysis of Balamuthia mandrillaris reveals potential virulence-related genes

Levinson, S. et al. Balamuthia mandrillaris brain infection: A rare cause of a ring-enhancing central nervous system lesion. Illustrative case. J. Neurosurg Case Lessons 3, 25 (2022). Google Scholar  Wu, X. et al. Diagnosing Balamuthia mandrillaris encephalitis via next-generation sequencing in a 13-year-old girl. Emerg. Microbes Infect. 9, 1379–1387 (2020)….

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i am having trouble with the VIBRANT embedded in Viroprofiler

Hi, I am trying to run the Viroprofiler, the new program to analyze viral metagenome data. Since the Viroprofiler encompasses multiple programs to run them all at once, I am facing error message after error message while running the command. While I was running my command as suggested, $nextflow run…

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phylogeny – Variation in 16S rRNA between assemblers – how do I know which is real?

I have a low-diversity metagenome (~11 bins > 80% completion). Out of the bins, 3 are of interest to me. None of the lower-completion bins that can be identified are from the group of interest. So let’s call the bins of interest 1, 2 and 3. The raw reads had…

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Potential pathogenicity of Non-O1, Non-O139 V. cholerae

Introduction Vibrio cholerae is a Gram-negative bacterium that can be classified into different serotypes based on the O surface antigen, with O1 and O139 being responsible for causing cholera in humans. Cholera is a highly infectious and severe diarrheal disease that is prevalent worldwide, particularly in Africa, South Asia, and…

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KEGG T31084: 3118

Entry 30322             CDS       T31084                                  Name OSD52_2014-06-21_1m_NPL022_spades_contig-30470_-_63_1127_orf-1   KO K00548   5-methyltetrahydrofolate–homocysteine methyltransferase [EC:2.1.1.13] Best hit pga:PGA1_c16040 (best score: 558.14) Taxonomy Alphaproteobacteria [GN:pga]Taxonomy Pathway 00270   Cysteine and methionine metabolism 00450   Selenocompound metabolism 00670   One carbon pool by folate 01100   Metabolic pathways 01110   Biosynthesis of secondary metabolites 01230   Biosynthesis of amino acids AA seq 354 aa…

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How/why contigs and scaffolds end up being identical in number and length by spades de novo assembly despite their different definitions

How/why contigs and scaffolds end up being identical in number and length by spades de novo assembly despite their different definitions 0 I encountered an issue while performing de novo assembly of phage genome reads (illumina paired end read) using SPAdes. I noticed that the number and length of contigs…

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Methylome evolution suggests lineage-dependent selection in the gastric pathogen Helicobacter pylori

Blow, M. J. et al. The epigenomic landscape of prokaryotes. PLoS Genet. 12, e1005854 (2016). Article  PubMed  PubMed Central  Google Scholar  Anton, B. P. & Roberts, R. J. Beyond restriction modification: epigenomic roles of DNA methylation in prokaryotes. Annu. Rev. Microbiol 75, 129–149 (2021). Article  PubMed  Google Scholar  Loenen, W….

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Genomic dissection of endemic carbapenem resistance reveals metallo-beta-lactamase dissemination through clonal, plasmid and integron transfer

Espedido, B. A., Partridge, S. R. & Iredell, J. R. bla(IMP-4) in different genetic contexts in Enterobacteriaceae isolates from Australia. Antimicrob. Agents Chemother. 52, 2984–2987 (2008). Article  CAS  PubMed  PubMed Central  Google Scholar  Kizny Gordon, A. et al. Genomic dynamics of species and mobile genetic elements in a prolonged blaIMP-4-associated…

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Large-scale analysis of flavivirus sequences, with no unknowns, in Aedes aegypti whole-genome DNA sequence data | Parasites and vectors

Spadar A, Phelan JE, Benavente ED, Campos M, Gomez LF, Mohareb F, et al. Flavivirus integration Aedes aegypti Limited and highly conserved across samples from different geographic regions, unlike integration Aedes albopictus. vectors of parasites. 2021; 14 (1): 332. Palatini U, Contreras CA, Gasmi L, Bonizzoni M. Endogenous viral elements…

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Large-scale reference-free analysis of flavivirus sequences in Aedes aegypti whole-genome DNA sequencing data

Spadar A, Phelan JE, Benavente ED, Campos M, Gomez LF, Mohareb F, et al. Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions in contrast to integrations in Aedes albopictus. Parasite vectors. 2021;14(1):332. Palatini U, Contreras CA, Gasmi L, Bonizzoni M. Endogenous viral…

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Large-scale reference-free analysis of flavivirus sequences in Aedes aegypti whole genome DNA sequencing data | Parasites & Vectors

Spadar A, Phelan JE, Benavente ED, Campos M, Gomez LF, Mohareb F, et al. Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus. Parasit Vectors. 2021;14(1):332. Palatini U, Contreras CA, Gasmi L, Bonizzoni M. Endogenous viral elements in…

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Genomic and phenotypic characterization of Acinetobacter colistiniresistens isolated from the feces of a healthy member of the community

Dwiyanto, J. et al. Pan-genome and resistome analysis of extended-spectrum ß-lactamase-producing Escherichia coli: A multi-setting epidemiological surveillance study from Malaysia. PLoS ONE 17, e0265142 (2022). Article  CAS  PubMed  PubMed Central  Google Scholar  Farrugia, D. N. et al. The complete genome and phenome of a community-acquired Acinetobacter baumannii. PLoS ONE 8,…

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Genome analysis of a coral-associated bacterial consortium highlights complementary hydrocarbon degradation ability and other beneficial mechanisms for the host

Fragoso Ados Santos, H. Impact of oil spills on coral reefs can be reduced by bioremediation using probiotic microbiota. Sci. Rep. doi.org/10.1038/srep18268 (2015). Article  PubMed  PubMed Central  Google Scholar  Silva, D. P. et al. Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and…

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Illumina short-read genome sequencing of knockout mutants in Streptococcus suis strain P1/7 constructed using pSStarget, a novel plasmid-based CRISPR/Cas9 genome editing system

Description: This dataset contains sequencing reads of the wild type strain S. suis P1/7 and two knockout mutants constructed using a novel CRISPR-Cas9 genome editing system for S. suis. Our data shows that our laboratory stock of strain P1/7 has 2 SNPs and one 5bp deletion relative to the reference…

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CamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter

Collins FS, Green ED, Guttmacher AE, Guyer MS. US National Human Genome Research Institute. A vision for the future of genomics research. Nature. 2003;422(6934):835–47. Article  CAS  PubMed  Google Scholar  Slatko BE, Gardner AF, Ausubel FM. Overview of next-generation sequencing technologies. Curr Protoc Mol Biol. 2018;122(1):e59. Article  PubMed  PubMed Central  Google…

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Global scale phylogeography of functional traits and microdiversity in Prochlorococcus

Costea PI, Munch R, Coelho LP, Paoli L, Sunagawa S, Bork P. metaSNV: a tool for metagenomic strain level analysis. PLoS ONE. 2017;12:1–9. Article  Google Scholar  Callahan BJ, McMurdie PJ, Holmes SP. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J. 2017;11:2639–43. Article  PubMed  PubMed…

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Coevolution of the Tlx homeobox gene with medusa development (Cnidaria: Medusozoa)

Chang, E. S. et al. Genomic insights into the evolutionary origin of Myxozoa within Cnidaria. Proc. Natl Acad. Sci. USA 112, 14912–14917 (2015). Article  CAS  PubMed  PubMed Central  Google Scholar  Boero, F. et al. Inconsistent Evolution and Paedomorphosis among the Hydroids and Medusae of the Athecatae/Anthomedusae and the Thecatae/Leptomedusae (Cnidaria,…

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Influence of mobile genetic elements and insertion sequences in long- and short-term adaptive processes of Acidithiobacillus ferrooxidans strains

Moya-Beltrán, A. et al. Genomic evolution of the class Acidithiobacillia: Deep-branching Proteobacteria living in extreme acidic conditions. ISME J. 15, 3221–3238 (2021). Article  PubMed  PubMed Central  Google Scholar  Nuñez, H. et al. Molecular systematics of the genus Acidithiobacillus: Insights into the phylogenetic structure and diversification of the taxon. Front. Microbiol….

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Searching for plasmid in assembly (plasmidSPAdes)

Searching for plasmid in assembly (plasmidSPAdes) 0 Hi, i am new to bioinformatics analysis and currently researching whole genome sequence of Acinetobacter baumannii. I used SPAdes to perform assembly of genome and plasmidSPAdes to do the same for plasmid. After that, BLASTn against PLSDB database were performed on plasmid assembly…

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KEGG T31096: 24216

Entry 56821             CDS       T31096                                  Name OSD65_2014-06-20_0.1m_NPL022_spades_contig-81008_-_453_821_orf-1   KO K07127   5-hydroxyisourate hydrolase [EC:3.5.2.17] Best hit mis:MICPUN_108340 (best score: 240.736) Taxonomy Green algae [GN:mis]Taxonomy Pathway 00230   Purine metabolism 01100   Metabolic pathways 01120   Microbial metabolism in diverse environments LinkDB All DBs AA seq 122 aa AA seqDB searchMGRSPITTHVLDTTRGRPAKDVPVTLATVSVADGSSWTVSGVTDADGRIADLLPVTHDLQPGVYVITFECEEYFRRTAAAYGVSGFYPKVSIHFEVKADQVKEHYHVPLLLNPYGYSTYRGS NT seq 369 nt NT seq  +upstreamnt  +downstreamntatggggcgatctcccatcaccacgcacgtgctggacacgacccgcggtcgacccgcgaaggatgtccccgtgactctcgccaccgtcagcgtggcggacgggtcctcgtggacggtcagcggcgtgaccgacgcggacgggcgcatcgccgatctcctcccagtcacgcacgacctacagcccggcgtgtacgtcataaccttcgagtgcgaggagtacttccggcgcaccgccgccgcgtacggggtctccgggttctacccaaaggtgtccatccacttcgaggtcaaggcggatcaggtcaaggagcactaccacgtcccactgctcctcaacccctatgggtacagcacgtacagaggcagctga Read more…

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Quast contig values not matching

Hello, I have recently generated a de novo fungal genome assembly using SPAdes. To gather some of the assembly statistics, I used QUAST Version: 5.0.2 with the following command: quast.py –fungus -o QuastResult ../SPAdesAssembly_UK0001.fasta I have checked the output from QUAST in the report.txt file, and I cannot work out…

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Whole-Genome Sequencing of Pseudomonas koreensis Isolated from Diseased Tor tambroides

Parte AC, Carbasse JS, Meier-Kolthoff JP et al (2020) List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 70(11):5607–5612. doi.org/10.1099/ijsem.0.004332 Article  PubMed  PubMed Central  Google Scholar  Duman M, Mulet M, Altun S et al (2021) The diversity of Pseudomonas species isolated…

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Introduction to Bioinformatics Tools for Sequencing and Analysis of Large-Scale Genomic Data

Bioinformatics is a field that combines biology, computer science, and statistics to analyze and interpret biological data. With the advent of high-throughput sequencing technologies, the amount of genomic data generated has increased exponentially. This has led to the development of bioinformatics tools that can handle large-scale genomic data and provide…

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Prevalence and clonal diversity of carbapenem-resistant Klebsiella pneumoniae causing neonatal infections: A systematic review of 128 articles across 30 countries

Citation: Hu Y, Yang Y, Feng Y, Fang Q, Wang C, Zhao F, et al. (2023) Prevalence and clonal diversity of carbapenem-resistant Klebsiella pneumoniae causing neonatal infections: A systematic review of 128 articles across 30 countries. PLoS Med 20(6): e1004233. doi.org/10.1371/journal.pmed.1004233 Received: July 13, 2022; Accepted: April 4, 2023; Published:…

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sage – Making card configurations in Sagemath

I’m following SageMath’s tutorial on Combinatorics and one of the exercizes is to calculate the set of Four of a Kind hands (in card games a hand containing four cards of the same value is called a four of a kind and a Hand is a subset of 5 cards)….

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Removing contamination from WGS nanopore reads prior to assembly

Removing contamination from WGS nanopore reads prior to assembly 1 Hello, I sent some isolated fungal DNA from a pure culture to a well-known sequencing company for sequencing using nanopore (promethion) and also illumina PE150 with the objective of generating a hybrid de-novo genome assembly using SPAdes. I assembled each…

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Highly drug resistant clone of Salmonella Kentucky ST198 in clinical infections and poultry in Zimbabwe

Anonymous. Tackling drug resistant infections globally: final report and recommendations. Review on Antimicrobial Resistance. amr-review.org/sites/default/files/160518_Final%20paper_with%20cover.pdf (2016). Antimicrobial Resistance C. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399, 629–655 (2022). Article  Google Scholar  Klein, E. Y. et al. Global increase and geographic convergence in antibiotic consumption…

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Antibiotics | Free Full-Text | Whole Genome Sequencing and Phenotypic Analysis of Antibiotic Resistance in Filifactor alocis Isolates

1. Introduction Filifactor alocis is an obligate anaerobic, non-sporeforming, Gram-positive rod [1,2]. This microorganism was first described in 1985 after being isolated from patients with periodontitis or gingivitis [3]. However, it was not until the early to mid-2000s, with the improvement of molecular identification techniques, when F. alocis was first…

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A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia

Grimont PAD, W. F. X. Antigenic formulae of the Salmonella serovars, 9th ed. (World health organization collaborating center for reference and research on Salmonella, Insitut Pasteur, 2007). Gal-Mor, O., Boyle, E. C. & Grassl, G. A. Same species, different diseases: how and why typhoidal and non-typhoidal Salmonella enterica serovars differ….

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Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes

Eme, L., Spang, A., Lombard, J., Stairs, C. W. & Ettema, T. J. G. Archaea and the origin of eukaryotes. Nat. Rev. Microbiol. 15, 711–723 (2017). Article  CAS  PubMed  Google Scholar  Spang, A. et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521, 173–179 (2015). Article …

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Options to use with inward stranded reverse (ISR) reads

Options to use with inward stranded reverse (ISR) reads 0 Hi, I would like to perform a differential gene expression analysis on my dataset. The dataset is made up of paired-end files, and the libraries are ISR type (inward stranded reverse reads). I’d like to be sure that I’m including…

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Error with dada2 while running Parkinson’s Mouse Tutorial – Technical Support

Hi, everyone. I’m new to qiime2 and I have a technical issue. I have the same problem with forum.qiime2.org/t/plugin-error-from-dada2-an-error-was-encountered-while-running-dada2-in-r-return-code-255/21016 when I ran Parkinson’s Mouse Tutorial, but I noticed the problem didn’t solved in the website above.That’s my error info: Plugin error from dada2: An error was encountered while running DADA2…

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Investigation of differences in susceptibility of Campylobacter jejuni strains to UV light-emitting diode (UV-LED) technology

Chlebicz, A. & Slizewska, K. Campylobacteriosis, salmonellosis, yersiniosis, and listeriosis as zoonotic foodborne diseases: A review. Int. J. Environ. Res. Public Health 15, 863 (2018). Article  PubMed  PubMed Central  Google Scholar  Soro, A. B., Whyte, P., Bolton, D. J. & Tiwari, B. K. Strategies and novel technologies to control Campylobacter…

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Acquisition and carriage of genetically diverse multi-drug resistant gram-negative bacilli in hospitalised newborns in The Gambia

United Nations Inter-agency Group for Child Mortality Estimation. Levels & Trends in Child Mortality: Report 2020, Estimates developed by the United Nations Inter-agency Group for Child Mortality Estimation. New York: United Nations Children’s Fund; 2020. Okomo, U. et al. Aetiology of invasive bacterial infection and antimicrobial resistance in neonates in…

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Genetic determinants of Biofilm formation of Helicobacter pylori using whole-genome sequencing | BMC Microbiology

Correa P, Houghton J. Carcinogenesis of Helicobacter pylori. Gastroenterology. 2007;133(2):659–72. Article  CAS  PubMed  Google Scholar  Dube C, Tanih N, Ndip R. Helicobacter pylori in water sources: a global environmental health concern. Rev Environ Health. 2009;24(1):1–14. Article  CAS  Google Scholar  Stark RM, Gerwig GJ, Pitman RS, Potts LF, Williams NA, Greenman…

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Comparative genome features and secondary metabolite biosynthetic potential of Kutzneria chonburiensis and other species of the genus Kutzneria

Adamek, M., Spohn, M., Stegmann, E. & Ziemert, N. Mining bacterial genomes for secondary metabolite gene clusters. Methods Mol. Biol. 1520, 23–47 (2017). CAS  PubMed  Google Scholar  Belknap, K. C., Park, C. J., Barth, B. M. & Andam, C. P. Genome mining of biosynthetic and chemotherapeutic gene clusters in Streptomyces…

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Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds

Asalone KC, Ryan KM, Yamadi M, Cohen AL, Farmer WG, George DJ, Joppert C, Kim K, Mughal MF, Said R, Toksoz-Exley M, Bisk E, Bracht JR (2020) Regional sequence expansion or collapse in heterozygous genome assemblies. PLoS Comput Biol. doi.org/10.1371/journal.pcbi.1008104 Article  PubMed  PubMed Central  Google Scholar  Bankevich A, Nurk S,…

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Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains

Kiu, R. & Hall, L. J. An update on the human and animal enteric pathogen Clostridium perfringens. Emerg. Microbes Infect. 7, 141 (2018). Article  PubMed  PubMed Central  Google Scholar  Li, J., Paredes-Sabja, D., Sarker, M. R. & McClane, B. A. Clostridium perfringens sporulation and sporulation-associated toxin production. Microbiol. Spectr. doi.org/10.1128/microbiolspec.TBS-0022-2015…

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Pangenomics of the death cap mushroom Amanita phalloides, and of Agaricales, reveals dynamic evolution of toxin genes in an invasive range

Sakai AK, Allendorf FW, Holt JS, Lodge DM, Molofsky J, With KA, et al. The population biology of invasive species. Annu Rev Ecol Syst. 2001;32:305–32. Article  Google Scholar  Allendorf FW, Lundquist LL. Introduction: population biology, evolution, and control of invasive species. Conserv Biol. 2003;17:24–30. Article  Google Scholar  Erickson AB. The…

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Apoptotic gene loss in Cnidaria is associated with transition to parasitism

Elmore, S. Apoptosis: A review of programmed cell death. Toxicol. Pathol. 35, 495–516 (2007). Article  CAS  PubMed  PubMed Central  Google Scholar  Shi, Y. Caspase activation, inhibition, and reactivation: A mechanistic view. Protein Sci. 13, 1979–1987 (2004). Article  CAS  PubMed  PubMed Central  Google Scholar  Alberts, B., Johnson, A. & Lewis, J….

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How to align Illumina FASTQ isolates to a conserved gene for phylogenetic analysis

How to align Illumina FASTQ isolates to a conserved gene for phylogenetic analysis 0 I am currently working on a project involving 100 isolates in Illumina FASTQ format. The objective of my study is to investigate the phylogenetic relationships among these isolates based on a conserved sequence within the HMG…

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Resistance of Nosocomial Acinetobacter baumannii

Chenxing Wei,1,* Jian Chen,1,* Tanveer Muhammad Anwar,2,* Lingling Huang,1 Wenjie Yang,3 Xueyan Dong,1 Qiong Chen,1 Min Yue,2,4,5 Daojun Yu1,3 1Department of Medical Laboratory, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People’s Republic of China; 2Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University…

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How could I filter a metagenomic assembly file (from Megahit or metaspades) for low coverage/short contigs to enable faster downstream analysis (i.e blastn)

How could I filter a metagenomic assembly file (from Megahit or metaspades) for low coverage/short contigs to enable faster downstream analysis (i.e blastn) 0 Title is pretty selg-explanatory, can i filter down a de-novo metagenomic assembly to make downstream analysis like blastn run faster? metagenomics blast spades megahit assembly •…

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Cuticle supplementation and nitrogen recycling by a dual bacterial symbiosis in a family of xylophagous beetles

Feldhaar H. Bacterial symbionts as mediators of ecologically important traits of insect hosts. Ecol Entomol. 2011;36:533–43. Article  Google Scholar  Douglas AE. Symbiosis as a general principle in eukaryotic evolution. Cold Spring Harb Perspect Biol. 2014;6:a016113–a016113. Article  PubMed  PubMed Central  Google Scholar  Flórez LV, Biedermann PHW, Engl T, Kaltenpoth M. Defensive…

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Subgenome-aware analyses suggest a reticulate allopolyploidization origin in three Papaver genomes

Reconstruction of gene and macro-synteny trees for the three studied Papaver species Syntenic blocks within the three Papaver species were identified with OrthoFinder v2.3.15. Orthologous and paralogous relationships, as well as orthogroups, were inferred using the parameters “-M msa -T fasttree” based on proteome sequences from multiple species. The resulting…

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Hot spring distribution and survival mechanisms of thermophilic comammox Nitrospira

Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, et al. Complete nitrification by Nitrospira bacteria. Nature 2015;528:504. Article  CAS  PubMed  PubMed Central  Google Scholar  van Kessel MA, Speth DR, Albertsen M, Nielsen PH, den Camp HJO, Kartal B, et al. Complete nitrification by a single microorganism….

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module ‘collections’ has no attribute ‘Hashable’

AttributeError: module ‘collections’ has no attribute ‘Hashable’ 0 Hello everyone I’m new using Spades and today I’m trying to do an assembly but I have a problem when I try to execute the pipeline. This is my script: spades.py -1 B_cepacia_raw_R1_paired.fastq.gz -2 B_cepacia_raw_R2_paired.fastq.gz -o spades_error_corrected_reads -t 50 -m 500 –only-error-correctio…

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CRISPR-resolved virus-host interactions in a municipal landfill include non-specific viruses, hyper-targeted viral populations, and interviral conflicts

Suttle, C. A. Environmental microbiology: Viral diversity on the global stage. Nat. Microbiol. 1, 16205 (2016). Article  CAS  PubMed  Google Scholar  Schulz, F. et al. Giant virus diversity and host interactions through global metagenomics. Nature 578, 432–436 (2020). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Dutilh, B. E., Reyes,…

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Complete genome analysis of African swine fever virus genotypes II, IX and XV from domestic pigs in Tanzania

Mason-D’Croz, D. et al. Modelling the global economic consequences of a major African swine fever outbreak in China. Nat. Food 1, 221–228 (2020). Article  PubMed  PubMed Central  Google Scholar  Sehl, J. et al. Comparative pathology of domestic pigs and wild boar infected with the moderately virulent African swine fever virus…

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