Tag: Metagenome

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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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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