Music of metagenomics—a review of its applications, analysis pipeline, and associated tools

No abstract is available for this paper.

• Publication year

  2021

• Venue

  Functional & Integrative Genomics

• Publication date

  2021-10-18

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1007/s10142-021-00810-yPMID 34657989
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Datasets

  2021cited by this paper
• Integrative Analysis of Fecal Metagenomics and Metabolomics in Colorectal Cancer

  2020cited by this paper
• SABIO-RK: database for biochemical reaction kinetics

  2020cited by this paper
• Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

  2020cited by this paper
• Statistical Framework

  2020cited by this paper
• ProteomicsDB: a multi-omics and multi-organism resource for life science research

  2019cited by this paper
• antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

  2019cited by this paper
• Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes

  2019cited by this paper
• DDBJ Database updates and computational infrastructure enhancement

  2019cited by this paper
• Ensembl 2020

  2019cited by this paper
• Decoding microbial community intelligence through metagenomics for efficient wastewater treatment

  2019cited by this paper
• WENGAN: Efficient and high quality hybrid de novo assembly of human genomes

  2019cited by this paper
• The power of small changes: Comprehensive analyses of microbial dysbiosis in breast cancer

  2019cited by this paper
• Nanopore Sequencing

  2019cited by this paper
• Genomics and metagenomics of colorectal cancer.

  2019cited by this paper
• Clinical metagenomics

  2019cited by this paper
• Fast and accurate long-read assembly with wtdbg2

  2019cited by this paper
• Anaerobic Biodegradation of Hydrocarbons: Metagenomics and Metabolomics

  2019cited by this paper
• The MACADAM database: a MetAboliC pAthways DAtabase for Microbial taxonomic groups for mining potential metabolic capacities of archaeal and bacterial taxonomic groups

  2019cited by this paper
• High accuracy DNA sequencing on a small, scalable platform via electrical detection of single base incorporations

  2019cited by this paper
• A Hybrid Feature Selection Method for Classifying Metagenomic Data in Relation to Inflammatory Bowel Disease

  2019cited by this paper
• The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters

  2018cited by this paper
• CoVaCS: a consensus variant calling system

  2018cited by this paper
• Bioprospecting of functional cellulases from metagenome for second generation biofuel production: a review

  2018cited by this paper
• HMMER web server: 2018 update

  2018cited by this paper
• Critical Assessment of Metagenome Interpretation Enters the Second Round

  2018cited by this paper
• The PRIDE database and related tools and resources in 2019: improving support for quantification data

  2018cited by this paper
• FROGS: Find, Rapidly, OTUs with Galaxy Solution

  2018cited by this paper
• pJRES Binning Algorithm (JBA): a new method to facilitate the recovery of metabolic information from pJRES 1H NMR spectra

  2018cited by this paper
• A-GAME: improving the assembly of pooled functional metagenomics sequence data

  2018cited by this paper
• Breast cancer in postmenopausal women is associated with an altered gut metagenome

  2018cited by this paper
• MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

  2018cited by this paper
• The Human Gut Microbiome – A Potential Controller of Wellness and Disease

  2018cited by this paper
• Bioaugmentation and biostimulation: a potential strategy for environmental remediation

  2018cited by this paper
• The microbiome in cancer immunotherapy: Diagnostic tools and therapeutic strategies

  2018cited by this paper
• UniProt: a worldwide hub of protein knowledge

  2018cited by this paper
• Assembly of long, error-prone reads using repeat graphs

  2018cited by this paper
• Metagenomic characterisation of ruminal bacterial diversity in buffaloes from birth to adulthood using 16S rRNA gene amplicon sequencing

  2018cited by this paper
• RNA-QC-chain: comprehensive and fast quality control for RNA-Seq data

  2018cited by this paper
• Accelerating metagenomic read classification on CUDA-enabled GPUs

  2017cited by this paper
• Faucet: streaming de novo assembly graph construction

  2017cited by this paper
• MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes

  2017cited by this paper
• miRPursuit—a pipeline for automated analyses of small RNAs in model and nonmodel plants

  2017cited by this paper
• MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads

  2017cited by this paper
• Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies

  2017cited by this paper
• AfterQC: automatic filtering, trimming, error removing and quality control for fastq data

  2017cited by this paper
• Fast and Simple Analysis of MiSeq Amplicon Sequencing Data with MetaAmp

  2017cited by this paper
• Metagenomics: novel enzymes from non‐culturable microbes

  2017cited by this paper
• Metabox: A Toolbox for Metabolomic Data Analysis, Interpretation and Integrative Exploration

  2017cited by this paper
• AMBER: Assessment of Metagenome BinnERs

  2017cited by this paper
• Improving contig binning of metagenomic data using \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ {d}_2^S $$\end{doc

  2017cited by this paper
• MetaCompass: Reference-guided Assembly of Metagenomes

  2017cited by this paper
• MegaGTA: a sensitive and accurate metagenomic gene-targeted assembler using iterative de Bruijn graphs

  2017cited by this paper
• A Novel Method for Predicting Ribosomal RNA Genes in Prokaryotic Genomes

  2017cited by this paper
• Reliable Biomarker discovery from Metagenomic data via RegLRSD algorithm

  2017cited by this paper
• A comprehensive quality control workflow for paired tumor‐normal NGS experiments

  2017cited by this paper
• BURRITO: An Interactive Multi-Omic Tool for Visualizing Taxa–Function Relationships in Microbiome Data

  2017cited by this paper
• A dysbiosis index to assess microbial changes in fecal samples of dogs with chronic inflammatory enteropathy

  2017cited by this paper
• ST Pipeline: an automated pipeline for spatial mapping of unique transcripts

  2017cited by this paper
• SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data

  2017cited by this paper
• fastQ_brew: module for analysis, preprocessing, and reformatting of FASTQ sequence data

  2017cited by this paper
• Large‐scale 16S gene assembly using metagenomics shotgun sequences

  2017cited by this paper
• Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data

  2017cited by this paper
• Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast

  2017cited by this paper
• Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

  2017cited by this paper
• Pheniqs: Fast and flexible quality-aware sequence demultiplexing

  2017cited by this paper
• De novo assembly of microbial genomes from human gut metagenomes using barcoded short read sequences

  2017cited by this paper
• Non-Covalent Functionalisation of C30 Fullerene by Pyrrole-n-Carboxylic Acid (n=2, 3): Density Functional Theory Studies

  2017cited by this paper
• Metaviz: interactive statistical and visual analysis of metagenomic data

  2017cited by this paper
• FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool

  2017cited by this paper
• Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies

  2017cited by this paper
• Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation

  2017cited by this paper
• MWASTools: an R/bioconductor package for metabolome-wide association studies

  2017cited by this paper
• MetaSort untangles metagenome assembly by reducing microbial community complexity

  2017cited by this paper
• PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies

  2017cited by this paper
• Reactome pathway analysis: a high-performance in-memory approach

  2017cited by this paper
• MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs)

  2017cited by this paper
• Zseq: An Approach for Preprocessing Next-Generation Sequencing Data

  2017cited by this paper
• Engineering Mycorrhizal Symbioses to Alter Plant Metabolism and Improve Crop Health

  2017cited by this paper
• Intestinal dysbiosis and probiotic applications in autoimmune diseases

  2017cited by this paper
• Scale-Invariant Biomarker Discovery in Urine and Plasma Metabolite Fingerprints.

  2017cited by this paper
• Biomartr: genomic data retrieval with R

  2017cited by this paper
• WormBase ParaSite − a comprehensive resource for helminth genomics

  2017cited by this paper
• NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis

  2017cited by this paper
• ProLanGO: Protein Function Prediction Using Neural Machine Translation Based on a Recurrent Neural Network

  2017cited by this paper
• Decontaminating eukaryotic genome assemblies with machine learning

  2017cited by this paper
• AFS: identification and quantification of species composition by metagenomic sequencing

  2017cited by this paper
• De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline

  2017cited by this paper
• ASAR: visual analysis of metagenomes in R

  2017cited by this paper
• Quality Assessment of High-throughput DNA Sequencing Data via Range analysis

  2017cited by this paper
• Hercules: a profile HMM-based hybrid error correction algorithm for long reads

  2017cited by this paper
• MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data

  2017cited by this paper
• Metagenomics for the Discovery of Novel Biosurfactants

  2017cited by this paper
• sigQC: A procedural approach for standardising the evaluation of gene signatures

  2017cited by this paper
• MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool

  2017cited by this paper
• MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle

  2017cited by this paper
• Genome composition and phylogeny of microbes predict their co-occurrence in the environment

  2017cited by this paper
• Semi‐automated cancer genome analysis using high‐performance computing

  2017cited by this paper
• BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly

  2016cited by this paper
• BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences.

  2016cited by this paper

• Microbiome Profiling in Chagas Disease: Sample Collection, Sequencing, and Analysis.

  2026cites this paper
• 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction

  2026cites this paper
• A review of neural networks for metagenomic binning

  2025cites this paper
• Computational Metagenomics: State of the Art

  2025cites this paper
• aXonica: A support package for MRI based Neuroimaging

  2024cites this paper
• TACKLING THE SOIL MICROBIOME – CHALLENGES AND OPORTUNITIES

  2024cites this paper
• A Review of Web-Based Metagenomics Platforms for Analysing Next-Generation Sequence Data

  2023cites this paper
• Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions

  2023influential citation
• Decoding the microbial universe with metagenomics: a brief insight

  2023cites this paper
• The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods

  2022cites this paper
• Detangling the Crosstalk Between Ascaris, Trichuris and Gut Microbiota: What´s Next?

  2022cites this paper