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Visualizing metagenomic and metatranscriptomic data: A comprehensive review.

作者信息

Aplakidou Eleni, Vergoulidis Nikolaos, Chasapi Maria, Venetsianou Nefeli K, Kokoli Maria, Panagiotopoulou Eleni, Iliopoulos Ioannis, Karatzas Evangelos, Pafilis Evangelos, Georgakopoulos-Soares Ilias, Kyrpides Nikos C, Pavlopoulos Georgios A, Baltoumas Fotis A

机构信息

Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece.

Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece.

出版信息

Comput Struct Biotechnol J. 2024 May 3;23:2011-2033. doi: 10.1016/j.csbj.2024.04.060. eCollection 2024 Dec.


DOI:10.1016/j.csbj.2024.04.060
PMID:38765606
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11101950/
Abstract

The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3649/11101950/56a0f545501e/gr5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3649/11101950/d69ff22bab61/ga1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3649/11101950/5fa5368789a7/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3649/11101950/4cb5796cd774/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3649/11101950/82ce668cd122/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3649/11101950/57538eb886c0/gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3649/11101950/56a0f545501e/gr5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3649/11101950/d69ff22bab61/ga1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3649/11101950/5fa5368789a7/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3649/11101950/4cb5796cd774/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3649/11101950/82ce668cd122/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3649/11101950/57538eb886c0/gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3649/11101950/56a0f545501e/gr5.jpg

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Visualizing metagenomic and metatranscriptomic data: A comprehensive review.

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[5]
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[6]
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本文引用的文献

[1]
Functional and evolutionary significance of unknown genes from uncultivated taxa.

Nature. 2024-2

[2]
Comparing methods for constructing and representing human pangenome graphs.

Genome Biol. 2023-11-30

[3]
SCALA: A complete solution for multimodal analysis of single-cell Next Generation Sequencing data.

Comput Struct Biotechnol J. 2023-10-20

[4]
RefSeq and the prokaryotic genome annotation pipeline in the age of metagenomes.

Nucleic Acids Res. 2024-1-5

[5]
SPIRE: a Searchable, Planetary-scale mIcrobiome REsource.

Nucleic Acids Res. 2024-1-5

[6]
metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data.

Gigascience. 2022-12-28

[7]
Unraveling the functional dark matter through global metagenomics.

Nature. 2023-10

[8]
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes.

Nucleic Acids Res. 2024-1-5

[9]
Fast and accurate identification of plasmids and viruses in sequencing data using geNomad.

Nat Biotechnol. 2024-8

[10]
BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes.

Microbiome. 2023-8-19

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