Tag: Metagenome

A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses

Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017). CAS  PubMed  Article  Google Scholar  Williams, T. A., Cox, C. J., Foster, P. G., Szöllősi, G. J. & Embley, T. M. Phylogenomics provides robust support for a two-domains tree of life. Nat. Ecol….

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Three families of Asgard archaeal viruses identified in metagenome-assembled genomes

Liu, Y. et al. Expanded diversity of Asgard archaea and their relationships with eukaryotes. Nature 593, 553–557 (2021). CAS  PubMed  Google Scholar  Dombrowski, N., Teske, A. P. & Baker, B. J. Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments. Nat. Commun. 9, 4999 (2018). PubMed  PubMed…

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A new approach produces a 90-fold increase in

Article Highlight | 15-Jun-2022 Researchers leverage viruses identified from worldwide environmental samples to expand knowledge of viral taxa and their role in tree microbiomes DOE/US Department of Energy image: Analysis of metatranscriptome samples with novel viral taxa in Populus. (Top) Graphical abstract of the pipeline. (Bottom) Percentage read classification with novel…

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RPKM, how to normalize for library size

RPKM, how to normalize for library size 1 Hi everybody! I’m working on several metagenomes (so not trascriptomes), and I mapped high quality reads to a database made of nucleotide sequences through bowtie2. I want to convert raw mapping counts of each gene in RPKM. I know this method might…

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How to normalize biom table from qiime2 to edgeR on Rstudio?

How to normalize biom table from qiime2 to edgeR on Rstudio? 0 Hi, I’m new in this of bioinformatics, I’m making a metagenome analysis of ITS region, then, I want to normalize my data, so i exported a biom table from qiime2 with taxonomic annotations, and then I converted that…

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DataSheet1_Enhancing Long-Read-Based Strain-Aware Metagenome Assembly.PDF

Microbial communities are usually highly diverse and often involve multiple strains from the participating species due to the rapid evolution of microorganisms. In such a complex microecosystem, different strains may show different biological functions. While reconstruction of individual genomes at the strain level is vital for accurately deciphering the composition…

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Get reference genome from Kraken2 taxID

Get reference genome from Kraken2 taxID 0 I have a ~10Gb ONT metagenome from citrus psyllid that I am trying to extract bacterial contigs from to assemble. My current thought for a pipeline is broadly as follows: Tentative ID of each contig with Kraken2, then QC to only take assignments…

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New Products Posted to GenomeWeb: MGI, Tecan, Qiagen, More

MGI HotMps High-Throughput Sequencing Kit BGI Group affiliate MGI has launched new commercial sequencing chemistry called HotMps for its DnbSeq-G400 sequencer. Built upon the combinatorial Probe Anchor Synthesis technology proprietary to MGI, HotMps can achieve low error rates, low duplication rates, and low index hopping while being compatible with commonly…

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Minimap2 detects too many 16S sequences in metagenome

16S is a very conserved sequence, which is why it’s used for targeted phylogenetic analysis; it makes it easy to amplify and analyse. Unfortunately that conservation is an issue with minimap2, which is built around the idea that matching scattered subsequences within a sequence is good enough for identifying matches…

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Metagenomics technology and microbial community diversity analysis methods

A large number of microorganisms in nature cannot be cultivated under laboratory conditions by pure culture methods, and the technical methods of traditional microbiology limit the research on environmental microorganisms. The rapid development of high-throughput omics technology has enabled humans to have an unprecedented understanding of the complex microbial communities…

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8. Metagenomic study_2022 (1).pdf – Week 8 Metagenomic study focusing on antibiotic resistance genes from food Metagenomics? The term “metagenomics” was

1Week 8Metagenomic study focusing on antibiotic resistance genes from foodMetagenomics?The term “metagenomics” was first used byJo Handelsman,Jon Clardy,Robert M. Goodman, Sean F.Brady, and others, and first appeared in publication in 1998. The term metagenome referenced the ideathat a collection of genessequenced from the environment could be analyzed in a way…

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Critical Assessment of Metagenome Interpretation: the second round of challenges

Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known…

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Uniref90 database – HUMAnN – The bioBakery help forum

Hello.I performed metagenome analysis using humann3 with the full UniRef90 database (20.7GB). I found many UniRef100-IDs in the file analyzed with UniRef90 database. Why are UniRef100-IDs included in Uniref90 database? Do I mistake anywhere?Thank you. Do you mean 1) that you saw IDs that looked like UniRef100_XYZ or 2) that…

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MG-RAST abundance values and filtering with SEEDs subsystem issue metagenome

Hi, I am working with annotating my metagenomes through the MG-RAST pipeline, annotating them with taxonomy and function. For this study we are interested in understanding phosphorus metabolism. To summarise, MG-RAST has a filtering option where you can filter by different levels in subsystems or refseq. When I use the…

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File No. of MG-RAST

File No. of MG-RAST 0 Does anyone know what kind of data ‘File 299.1’ in MG-RAST? While I was downloading raw data by specifying ‘File 050.1’, some came out with error {“ERROR”:”requested file (050.1) is suppressed; try file=299.1″} Can’t find out what kind of data 299.1 would be. MG-RAST Metagenome…

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Frontiers | Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation

Introduction The study of the microbial environments has benefited from the sequencing revolution, where technology improvement decreased the DNA sequencing cost and increased the number of sequenced nucleic bases. For approximately 20 years (depending on how we define the term metagenomics), it has allowed the decryption of the microbial composition…

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Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics | Environmental Microbiome

Steen AD, Crits-Christoph A, Carini P, DeAngelis KM, Fierer N, Lloyd KG, Cameron TJ. High proportions of bacteria and archaea across most biomes remain uncultured. ISME J. 2019;13:3126–30. PubMed  PubMed Central  Google Scholar  Goh KM, Shahar S, Chan K-G, Chong CS, Amran SI, Sani MH, Zakaria II, Kahar UM. Current…

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Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM

Wu, W. et al. NDM metallo-β-lactamases and their bacterial producers in health care settings. Clin. Microbiol. Rev. 32, e00115–18 (2019). Yong, D. et al. Characterization of a new metallo-β-lactamase gene, bla NDM-1, and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14…

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HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps

doi: 10.1186/s13059-022-02626-w. Affiliations Expand Affiliations 1 Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA. 2 Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA. fsun@usc.edu. Item in Clipboard Yuxuan Du et al. Genome Biol. 2022. Show details Display options Display options Format…

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Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis

INTRODUCTION Next-generation sequencing (NGS) has revolutionized many areas of biological research (1, 2), providing ever-more data at an ever-decreasing cost. One such area is microbiome research, the study of microbes in their theater of activity using metagenomic sequencing (3). Here, deep short-read sequencing, and improving performance of long-read sequencing, are…

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Screening methods optimal to sequence marine metagenome for understanding carbon dioxide fixation. Introduction: The study of genetic material that is specifically extracted from environmental samples is termed as metagenomics. Conventional microbiology and microbial genome sequencing along with genomics depend on cultivated clonal culture. On the other hand, early sequencing of environmental genes performs cloning of specific genes via the 16S (Svedberg unit) rRNA (ribosomal ribonucleic acid) gene in order to generate a diversity profile in a natural sample.

1 Microbial Life: Origin And Discovery2 Observing The Microbial Cell3 Cell Structure And Function4 Bacterial Culture, Growth, And Development5 Environmental Influences And Control Of Microbial Growth6 Viruses7 Genomes And Chromosomes8 Transcription, Translation, And Bioinformatics9 Gene Transfer, Mutations, And Genome Evolution10 Molecular Regulation11 Viral Molecular Biology12 Biotechniques And Synthetic Biology13 Energetics…

Continue Reading Screening methods optimal to sequence marine metagenome for understanding carbon dioxide fixation. Introduction: The study of genetic material that is specifically extracted from environmental samples is termed as metagenomics. Conventional microbiology and microbial genome sequencing along with genomics depend on cultivated clonal culture. On the other hand, early sequencing of environmental genes performs cloning of specific genes via the 16S (Svedberg unit) rRNA (ribosomal ribonucleic acid) gene in order to generate a diversity profile in a natural sample.

New method and model address blindspot toward

New method and model address blindspot towards uncommon species in mixed samples For higher accuracy and more effective microbial diagnostics, researchers at the Earlham Institute have evaluated a new approach to analyse metagenomic samples that may contain low numbers of certain species – helping to prevent crucial genomic information from…

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Critical assessment of pan-genomics of metagenome-assembled genomes

Abstract 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,…

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FastQC analysis

FastQC analysis 0 Hii, Could anyone please tell me if I can carry out the FastQC analysis using data available online and not in my system? The sequence data that I want to check is huge so was wondering if there was any way to access them online through FastQC?…

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Assistant Professor of bioinformatics and metagenomics at Novo Nordisk Foundation Center for Protein Research

Job title: Assistant Professor of bioinformatics and metagenomics at Novo Nordisk Foundation Center for Protein Research Company: Workscout Job description Job beskrivelse We are looking for a highly motivated and dynamic Assistant Professor for a 4-year position to commence on the 1st of April 2022 or soon hereafter. The position…

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Assistant Professor Job – Bioinformatics and Metagenomics, UCPH, Denmark, Jan 2022

The University of Copenhagen invites applications for an Assistant Professor position will be in the Human Proteome Variation group at The Novo Nordisk Foundation Center for Protein Research, Denmark – Jan 2022 Qualification Details Six overall criteria apply for Assistant Professor appointments at the University of Copenhagen. The six criteria…

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metagenome low alignment rate

metagenome low alignment rate 1 I have 20 metagenome samples which need to be analyzed. I started with one sample for the time being with the below tools/pipelines. After assembling first sample I mapped its reads back to contigs but the alignment rate is pretty low, What could be the…

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Researchers identify new bacteria and viruses in human skin

Data representing a variety of microorganisms found in the human skin microflora. Credits: Karen Arnott / EMBL Researchers and colleagues at EMBL’s European Bioinformatics Institute (EMBL-EBI), National Institutes of Health (NIH) National Institute for Human Genome (NHGRI), NIH National Institute for Arthritis, Musculoskeletal and Skin Diseases are new bacteria and…

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Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome

1. Wang, J. & Jia, H. Metagenome-wide association studies: fine-mining the microbiome. Nat. Rev. Microbiol. 14, 508–522 (2016). CAS  PubMed  Google Scholar  2. Moschen, A. R. et al. Lipocalin 2 protects from inflammation and tumorigenesis associated with gut microbiota alterations. Cell Host Microbe 19, 455–469 (2016). CAS  PubMed  Google Scholar …

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Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions

1. Oh, J. et al. Biogeography and individuality shape function in the human skin metagenome. Nature 514, 59–64 (2014). 2. Byrd, A. L., Belkaid, Y. & Segre, J. A. The human skin microbiome. Nat. Rev. Microbiol. 16, 143–155 (2018). CAS  PubMed  Google Scholar  3. Oh, J. et al. Temporal stability…

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Long read de novo phylogenetic tree for metagenome

Long read de novo phylogenetic tree for metagenome 0 What tools are available to create de novo phylogenetic trees for long read metagenome datasets? phyloT seems to construct one based on taxonomy and NCBI/GTDb information rather than read alignment. Is MAFFT commonly used? What is the standard methodology? (For reference,…

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About QUAST

About Short intro Further reading How to cite Brief project history Authors Funding License and Terms of use Short intro QUAST evaluates genome assemblies by computing various metrics, including N50, length for which the collection of all contigs of that length or longer covers at least 50% of assembly length…

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vRhyme enables binning of viral genomes from metagenomes

Abstract Genome binning has been essential for characterization of bacteria, archaea, and even eukaryotes from metagenomes. Yet, no approach exists for viruses. We developed vRhyme, a fast and precise software for construction of viral metagenome-assembled genomes (vMAGs). vRhyme utilizes single- or multi-sample coverage effect size comparisons between scaffolds and employs…

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Dryad Data — Lichen fungi do not depend on the alga for ATP production

Lichen fungi live in a symbiotic association with unicellular phototrophs and have no known aposymbiotic stage. A recent study postulated that some of them have lost mitochondrial oxidative phosphorylation and rely on their algal partners for ATP. This claim originated from an apparent lack of ATP9, a gene encoding one subunit…

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Towards the biogeography of prokaryotic genes

1. Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015). PubMed  Google Scholar  2. Zou, Y. et al. 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses. Nat. Biotechnol. 37, 179–185 (2019). CAS  PubMed  PubMed Central  Google Scholar  3. Mohammad,…

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Redundancy analysis (RDA) for metagenomic community

Redundancy analysis (RDA) for metagenomic community 0 Hello I want to do Redundancy analysis (RDA) to see variation in my bacterial community samples but I am kinda lost and don’t know where to start. I searched online but couldn’t find any. Is there any R code or tutorial available for…

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Genomics and informatics, conjoined tools vital for understanding and protecting plant health

This article was originally published here Phytopathology. 2021 Dec 10. doi: 10.1094/PHYTO-10-21-0418-RVW. Online ahead of print. ABSTRACT Genomics’ impact on crop production continuously expands. The number of sequenced plant and microbial species and strains representing diverse populations of individual species rapidly increases thanks to the advent of next generation sequencing…

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BRAIN Biotech AG: Additional Genome Editing Nuclease: BRAIN-Metagenome-Cas 01 (BMC01)

DGAP-News: BRAIN Biotech AG / Key word(s): Miscellaneous/Patent08.12.2021 / 15:00 The issuer is solely responsible for the content of this announcement. Zwingenberg, Germany, December 8th, 2021 Additional Genome Editing Nuclease: BRAIN-Metagenome-Cas 01 (BMC01) BRAIN Biotech AG has successfully extended its proprietary genome editing toolbox with the addition of BRAIN-Metagenome-Cas 01…

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Discovery and Biosynthesis of Natural Products from New Zealand Soil Metagenome Libraries

Antibiotic discovery rates dramatically declined following the “golden age” of the 1940’s to the 1960’s. The platforms that underpinned that age of discovery rested upon laboratory cultivation of a small clade of bacteria, the actinomycetes, primarily isolated from soil environments. Fermentation extracts of these isolated bacteria have provided the majority…

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Adapting Macroecology to Microbiology: Using Occupancy Modeling To Assess Functional Profiles across Metagenomes

doi: 10.1128/mSystems.00790-21. Online ahead of print. Affiliations Expand Affiliation 1 Department of Biology, University of Waterloo, Waterloo, Ontario, Canada. Item in Clipboard Angus S Hilts et al. mSystems. 2021. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1128/mSystems.00790-21. Online ahead of print. Affiliation 1 Department of Biology, University of Waterloo,…

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BRAIN Biotech AG: Additional Differentiated Genome-Editing Nuclease: BRAIN-Metagenome-Cas 01 (BMC01)

DGAP-Ad-hoc: BRAIN Biotech AG / Key word(s): Miscellaneous/PatentBRAIN Biotech AG: Additional Differentiated Genome-Editing Nuclease: BRAIN-Metagenome-Cas 01 (BMC01) 08-Dec-2021 / 14:53 CET/CESTDisclosure of an inside information acc. to Article 17 MAR of the Regulation (EU) No 596/2014, transmitted by DGAP – a…

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Metagenome-genome-wide association studies reveal human genetic impact on the oral microbiome

The oral microbiota contains billions of microbial cells, which could contribute to diseases in many body sites. Challenged by eating, drinking, and dental hygiene on a daily basis, the oral microbiota is regarded as highly dynamic. Here, we report significant human genomic associations with the oral metagenome from more than…

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Scripts for BGC analysis in large MAGs and results of their application to soil metagenomes within Chernevaya Taiga RSF-funded project

This repository include scripts for analysis of biosynthetic gene clusters (BGCs) in large metagenome assemblies. All scripts were created within the Chernevaya Taiga project funded by the Russian Science Foundation (grant 19-16-00049). The repository also contains results of the scripts application to four hybrid (illumina + ONT) assemblies of various…

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how to create a custom database (GTDB) ?

how to create a custom database (GTDB) ? 0 Hello I was asked for creating a custom database from GTDB, I just need to incorporate some metagenome assembly genomes (MAGs) to the GTDB database the issue is that I dont know how to do that. the GTDB file “gtdbtk_data.tar.gz” from…

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Searching metagenomic datasets for a specific species

Searching metagenomic datasets for a specific species 1 Hi, There are a vast number of metagenomic datasets available from microbiomes in different environments, such as marine, terrestrial, human, etc. These datasets seem to capture a massive amount of data relating to community composition. As such, I am wondering if there…

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Postdoc in bioinformatics and metagenomics at Novo Nordisk Foundation Center for Protein Research – University of Copenhagen – job portal

Job Portal Postdoc in bioinformatics and metagenomics at Novo Nordisk Foundation Center for Protein Research We are looking for a highly motivated and dynamic researcher for a 2 year position, to commence on 1 January 2022 or soon hereafter. The position will be in the Human Proteome Variation group at The Novo Nordisk…

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Jobot hiring Bioinformatics Scientist in St Louis, Missouri, United States

Bioinformatics Scientist – Agricultural DNA Extraction!This Jobot Job is hosted by Drew J. Fibus Are you a fit? Easy Apply now by clicking the “Apply” button and sending us your resume. Salary $75,000 – $130,000 per year A Bit About Us Based in St. Louis, MO with 2 offices across…

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Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis

1. Hackstein JH, Stumm CK. Methane production in terrestrial arthropods. Proc Natl Acad Sci USA. 1994;91:5441–5. CAS  PubMed  PubMed Central  Article  Google Scholar  2. Hackstein JHP, van Alen TA. Fecal methanogens and vertebrate evolution. Evolution. 1996;50:559–72. PubMed  Article  PubMed Central  Google Scholar  3. Borrel G, McCann A, Deane J, Neto…

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Postdoctoral Research Scientist (Integrated Microbiomics Bioinformatics) at Earlham Institute

Applications are invited for a Postdoctoral Research Scientist to join the Laboratory of Dr Chris Quince in the High-Resolution Microbiomics group at the Earlham Institute, based in Norwich, UK.   Background: The High-resolution Microbiomics group focusses on both theoretical and experimental methods for microbial community analysis. Combining statistical bioinformatics with…

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Postdoctoral Fellow in Bioinformatics Job in North Carolina (NC), Higher-Ed/Education Career, Jobs in University of North Carolina at Charlotte

Postdoctoral Fellow in BioinformaticsUNC Charlotte – Charlotte, NC The Department of Bioinformatics and Genomics at the University of North Carolina at Charlotte seeks a post-doctoral fellow to work under the supervision of Dr. Anthony Fodor. The successful applicant will work on NIH supported projects that investigate the role of…

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PhD position ‘Virus diversity and evolution in natural plant ecosystems’

Category Research / Academic Location Wageningen You might share our view that wild plant communities might act as viral reservoirs that are also connected to agricultural plants. Since viruses can spill over from natural to agricultural systems, it is highly relevant to characterize virus diversity in wild plants. Plant virus…

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How does MetaProdigal handle metagenomics where different genetic codes are used?

How does MetaProdigal handle metagenomics where different genetic codes are used? 1 I’m wondering how prodigal when using -p meta can handle genes from different genetic codes? For example, if Gracilibacteria/SR1 was in there it would use genetic code 25. Would it catch this? When running in meta mode does…

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Postdoctoral researcher Microbiome Bioinformatics 100%, Zurich, fixed-term

Postdoctoral researcher Microbiome Bioinformatics 100%, Zurich, fixed-term 100%, Zurich, fixed-term The Food Systems Biotechnology (FSB) group is seeking a postdoctoral researcher with expertise in microbiome metagenomics and bioinformatics to lead efforts for characterization and analysis of global microbial biodiversity as part of the Microbiota Vault initiative’s efforts to preserve our microbial…

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How to compute module completion ratio of KEGG modules from KO identifiers? (command line)

How to compute module completion ratio of KEGG modules from KO identifiers? (command line) 0 I was previously using KEGG-MAPLE to compute module completion ratios for metagenome assembled genomes. However, this tool was web only (very frustrating) and also it has been discontinued. Now I’m trying to do something similar…

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Postdoctoral researcher: Microbiome Bioinformatics

In der aktuellen Covid-19 Situation laufen die Rekrutierungen weiter. Es kann dabei allerdings zu Verzögerungen kommen. Vielen Dank für Ihr Verständnis. 100%, Zurich, fixed-term The Food Systems Biotechnology (FSB) group is seeking a postdoctoral researcher with expertise in microbiome metagenomics and bioinformatics to lead efforts for characterization and analysis of global…

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WGS bacterial metagenomic pipeline – group comparison

WGS bacterial metagenomic pipeline – group comparison 0 Hello all, I was wondering what’s the recent state-of-the-art pipeline to do metagenome comparison, with multiple samples and groups? E.g. I have several “patients” and several “controls” in the form of WGS reads, and I want to run a comparison (on some…

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Mapping reads and quantifying genes

Mapping reads and quantifying genes – Metagenomic workshop 0 Hello, I am using the following metagenomic workshop tutorial to analyse my own metagenomic data. metagenomics-workshop.readthedocs.io/en/latest/annotation/quantification.html I performed the following steps: mapped reads with bowtie2 and generated .bam file with samtools sort. Removed duplicates with picard Extracted gene information from prokka…

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Genomics Data Scientist

Genomics Data Scientist – 93419 Organization: JG-Joint Genome Institute Lawrence Berkeley National Lab (LBL, lbl.gov/) Joint Genome Institute (JGI, jgi.doe.gov/) Division has an opening for a Genomics Data Scientist. This is an exciting opportunity for applying your data science expertise in genomics to solve the most challenging energy and environmental…

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How to search for species with certain function or pathway in the annotated genome?

How to search for species with certain function or pathway in the annotated genome? 0 I’m trying to find bacterial species with certain metabolic pathways. I want to curate a “metagenome” of individual species that each have certain metabolic characteristics. So far, I have found KEGG has information on metabolic…

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SRA splitting for each metagenome-assembled genome

Job:SRA splitting for each metagenome-assembled genome 0 Hi everybody, we obtained viruses from water and sequenced them with Illumina. we formed different metagenomic-assembled genomes and get a Bioproject number and Biosample numbers (for each of them). Now, i should do SRA submission. But i cannot submit for my all genomes…

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