Tag: MetaPhlAn2

Error in Locally Cached for MetaPhlAn2 and HUMAnN2 – usegalaxy.be support

Hi there, I am using galaxy for a university project and I have noticed that since the update some elements of the tools I need for it don’t function as they did before. The two that I primarily noticed was when using MetaPhlAn2 and HUMAnN2. For both of them the…

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Gut Microbiome of Children with Airway Allergic Disease

Introduction Allergic airway diseases affect many people worldwide, and incidences are still increasing gradually. Allergic rhinitis and allergic asthma, are typical chronic nasopharyngitis respiratory diseases in pediatric, causing an enormous burden of illness and high economic costs to the community.1 Allergic rhinitis and allergic asthma are immunoglobulin E (IgE)-mediated inflammatory…

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Metaphlan2 phylogenetic tree – MetaPhlAn

Jen May 15, 2023, 4:00pm 1 I’m looking for/trying to make a phylogenetic tree for data analyzed originally by metaphlan 2. I can make the tree using the marker database, but the link to the marker database on the metaphlan 2 page is broken. Can someone point me to where…

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Introduction to R for Microbiome Data

Abubucker, Sahar, Nicola Segata, Johannes Goll, Alyxandria M. Schubert, Jacques Izard, Brandi L. Cantarel, Beltran Rodriguez-Mueller, Jeremy Zucker, Mathangi Thiagarajan, Bernard Henrissat, Owen White, Scott T. Kelley, Barbara Methé, Patrick D. Schloss, Dirk Gevers, Makedonka Mitreva, and Curtis Huttenhower. 2012. Metabolic reconstruction for metagenomic data and its application to the…

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Normalizing before Metaphlan2

Normalizing before Metaphlan2 1 Hello, I am had run Metphlan2 to understand the relative abundance of some organisms in three of my samples. I have differences in the number of reads in the samples after Quality control. Do I need to normalizing the reads? Will normalizing the reads with depth…

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Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes

Blume-Werry G, Krab EJ, Olofsson J, Sundqvist MK, Väisänen M, Klaminder J. Invasive earthworms unlock arctic plant nitrogen limitation. Nat Commun. 2020;11:1766. Article  CAS  PubMed  PubMed Central  Google Scholar  Xing Y, Meng X, Wang L, Zhang J, Wu Z, Gong X, et al. Effects of benzotriazole on copper accumulation and…

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Metagenomics – Texas A&M HPRC

Back to Bioinformatics Main Menu Mothur GCATemplates available: no Mothur homepage module spider Mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities See syntax for commands when running in command line mode such as in a batch file. mothur.org/wiki/Command_line_mode QIIME GCATemplates available: terra QIIME is an open-source bioinformatics pipeline for…

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Index of /ubuntu/pool/universe/m/metaphlan2-data/

../ metaphlan2-data_2.6.0+ds-3.debian.tar.xz 05-Dec-2017 17:30 8048 metaphlan2-data_2.6.0+ds-3.dsc 05-Dec-2017 17:29 2066 metaphlan2-data_2.6.0+ds-3_all.deb 05-Dec-2017 23:20 195M metaphlan2-data_2.6.0+ds-4.debian.tar.xz 11-Dec-2018 17:13 8476 metaphlan2-data_2.6.0+ds-4.dsc 11-Dec-2018 17:13 2046 metaphlan2-data_2.6.0+ds-4_all.deb 11-Dec-2018 17:29 195M metaphlan2-data_2.6.0+ds.orig.tar.xz 02-Nov-2016 03:22 194M Read more here: Source link

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Exploiting a targeted resistome sequencing approach in assessing antimicrobial resistance in retail foods | Environmental Microbiome

O’Neill J. The Review on Antimicrobial Resistance—tackling drug-resistant infections globally: final report and recommendations. 2016. Murray CJ, Ikuta KS, Sharara F, Swetschinski L, Robles Aguilar G, Gray A, et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. The Lancet. 2022;399:629–55. Article  CAS  Google Scholar  Laxminarayan R….

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Multi-faceted metagenomic analysis of spacecraft associated surfaces reveal planetary protection relevant microbial composition

. 2023 Mar 22;18(3):e0282428. doi: 10.1371/journal.pone.0282428. eCollection 2023. Sarah K Highlander  1 , Jason M Wood  2 , John D Gillece  1   3 , Megan Folkerts  1 , Viacheslav Fofanov  3   4 , Tara Furstenau  3 , Nitin K Singh  2 , Lisa Guan  2 , Arman Seuylemezian  2 , James N Benardini  2 , David M Engelthaler …

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JPL study uses metagenomic sequencing to monitor microbial burden on spacecraft

A recent study published in the journal PLOS ONE uses metagenomics to examine the microbial composition in samples obtained from the Jet Propulsion Laboratory (JPL). Study: Multi-faceted metagenomic analysis of spacecraft-associated surfaces reveal planetary protection relevant microbial composition. Image Credit: Gorodenkoff / Shutterstock.com Maintaining the cleanliness of spacecraft The JPL has several metagenomically-monitored…

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CRITICAL ERROR: The metaphlan2.py executable can not be found – MetaPhlAn

Hi all, I am trying to run humann2 and get this error: (primate) root@DESKTOP-J59VIIJ:/mnt/c/Users/samde/gutmicrobiome# humann2 –input primateFastq/kneadpaired/KIT_HANDLER_DN_MG3_D8.filt1_kneaddata_paired_1.fastq –output humOut/KIT_HANDLER_DN_MG3_D8.filt1_kneaddata_paired_1 –threads 3Output files will be written to: /mnt/c/Users/samde/gutmicrobiome/humOut/KIT_HANDLER_DN_MG3_D8.filt1_kneaddata_paired_1CRITICAL ERROR: The metaphlan2.py executable can not be found. Please check the install. There is a similar post saying to run metaphlan2.py –version But…

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How To Install metaphlan2 on Ubuntu 20.04

In this tutorial we learn how to install metaphlan2 on Ubuntu 20.04. metaphlan2 is Metagenomic Phylogenetic Analysis 3b2f7f0abf7727c8176639b50ed2f548 Introduction In this tutorial we learn how to install metaphlan2 on Ubuntu 20.04. What is metaphlan2 metaphlan2 is: MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea,…

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comparing two metagenomics data sets

comparing two metagenomics data sets 2 Hello all, I have a shotgun metagenomic dataset (20 samples) paired-end reads. I want to compare my data to another dataset published and available online. I am confused as how can I do it. Please let me know if you have an idea. Thanks…

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Comparison of fecal and blood metabolome reveals inconsistent associations of the gut microbiota with cardiometabolic diseases

Study cohorts This study was based on the Guangzhou Nutrition and Health Study (GNHS). The detailed description of GNHS cohort could be found in previous studies22,23. Briefly, a total of 4048 Chinese participants aged 40–75 years living in the urban area of Guangzhou, China, for at least 5 years were…

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Page Not Found – The bioBakery help forum

The bioBakery help forum Sign Up Log In Log In Popular Announcing MetaPhlAn 4MetaPhlAn Announcing HUMAnN 3.5HUMAnN Clear guidance needed for comparing across samples with varying sequencing depthMetaPhlAn List of taxa in Metaphlan4 databaseMetaPhlAn Metaphlan 4 install issueMetaPhlAn ERROR: The MetaPhlAn2 taxonomic profile provided was not generated with the database…

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MetaPhlAn2 – BioGrids Consortium – Supported Software

AllHigh-Throughput SequencingGenomicsProteomicsVisualizationOther MetaPhlAn2 Description (Metagenomic Phylogenetic Analysis) is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. Installation Use the following command to install this title with the CLI client: $ biogrids-cli install metaphlan2 Copy to clipboard Primary Citation* N. Segata, L. Waldron, A….

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