Tag: mothur

16s rRNA Sequencing Meta-analysis Reconstruction Tool (using mothur).

16SMaRT is a bioinformatics analysis pipeline for 16s rRNA gene sequencing data. 16SMaRT is a “one-click” solution towards performing microbial community analysis of amplicon sequencing data. 16SMaRT aims to be your go-to solution for your next microbiome/metagenomics project. The primary objective of 16SMaRT analysis is to determine what genes are…

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Skin microbiome composition & diversity in Atopic dermatitis

Introduction Atopic dermatitis (AD) is the most common chronic, and recurrent inflammatory skin disease. The prevalence of AD varies throughout the world and still increasing. In developing countries, 10–20% of children and 1–3% of adults are affected by AD. This disease is characterized by significant itching.1,2 Intense itching causes trauma…

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Clustering in virome

Clustering in virome 0 Please, can someone suggest to me a bioinformatics tool for de-novo clustering in virome? I would like to use DADA2 (as AVS clustering tool) plugin of QIIME2, but it looks specific for 16S rRNA gene amplicon sequencing and I am not sure it will work well…

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Bug#984243: Help: mothur: ftbfs with GCC-11

Hi Andreas, Andreas Tille, on 2021-10-21: > In file included from addtargets2.cpp:3: > myutils.h:176:1: error: reference to ‘byte’ is ambiguous Since C++ 2017, the std::byte type is defined: > 176 | byte *ReadAllStdioFile(FILE *f, off_t &FileSize); > | ^~~~ > In file included from /usr/include/c++/11/bits/stl_algobase.h:61, > from /usr/include/c++/11/bits/char_traits.h:39, > from…

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The Profile and Function of Gut Microbiota in Diabetic Nephropathy

Introduction Diabetic nephropathy (DN) is characterized by kidney function loss caused by diabetes mellitus.1 Almost one-third of patients with diabetes have DN, and the prevalence of DN is increasing worldwide.2 DN is one of the most important factors of chronic kidney disease and end-stage renal disease (ESRD). The signs and…

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[Solved] tatements are true about the commands used in mothur during the process of generating contigs, filtering and merging the contigs and countin…

Which of the following statements are true about the commands used… in mothur during the process of generating contigs, filtering and merging the contigs and counting contigs?Question 17 options: The make.contigs command will extract the sequence and quality score data from your fastq files, create the reverse complement of the…

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deseq2 tutorial microbiome

phyloseq Handling and analysis of high-throughput microbiome census data. Detecting the periodontal pathogens at the subgingival plaque requires skilled professionals to collect samples. Import mothur list and group files and return an otu_table. In a randomized, double-blind, placebo-controlled trial, we assessed the effect of Lactobacillus reuteri supplementation, from birth to…

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Mother update request – Galaxyproject/Tools-Iuc

Dear Galaxy maintainers, I would like to ask for an update of the Mothur version on the usegalaxy server.Currently the installed version is 1.39.5.0, whereas the latest version is 1.46.1 (on mothur.org). The more recent version allows for converting DADA2 count table output to shared data format using the command…

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Add ASV/OTU to taxonomy string for sequences

Ask questionsAdd ASV/OTU to taxonomy string for sequences forum.mothur.org/t/otu-and-asv-in-taxonomy-file/20988 mothur/mothur Answer questions Preliminary output example: ASV_OTULabel ASV_Abundance Taxonomy_Clustered_OTULabel Otu0001 12196 Bacteria;”Bacteroidetes”;”Bacteroidia”;”Bacteroidales”;”Porphyromonadaceae”;”Porphyromonadaceae”_unclassified;Otu001; Otu0002 8829 Bacteria;”Bacteroidetes”;”Bacteroidia”;”Bacteroidales”;”Porphyromonadaceae”;”Porphyromonadaceae”_unclassified;Otu002; … Otu0331 4 Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Lachnospiraceae_unclassified;Otu041; Otu0332 4 Bacteria;”Bacteroidetes”;”Bacteroidia”;”Bacteroidales”;”Porphyromonadaceae”;”Porphyromonadaceae”_unclassified;Otu005; Otu0333 4 Bacteria;”Proteobacteria”;Gammaproteobacteria;Pseudomonadales;Moraxellaceae;Acinetobacter;Otu259; Otu0334 4 Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Lachnospiraceae_unclassified;Otu187; … Otu2423 1 Bacteria;”Bacteroidetes”;”Bacteroidia”;”Bacteroidales”;”Porphyromonadaceae”;”Porphyromonadaceae”_unclassified;Otu012; Otu2424 1 Bacteria;Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Oscillibacter;Otu175; useful! Read more here: Source link

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