Literature DB >> 34657989

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

Bilal Wajid1,2,3,4, Faria Anwar5, Imran Wajid6,7, Haseeb Nisar8,9, Sharoze Meraj6, Ali Zafar6, Mustafa Kamal Al-Shawaqfeh10, Ali Riza Ekti11, Asia Khatoon9, Jan S Suchodolski12.   

Abstract

This humble effort highlights the intricate details of metagenomics in a simple, poetic, and rhythmic way. The paper enforces the significance of the research area, provides details about major analytical methods, examines the taxonomy and assembly of genomes, emphasizes some tools, and concludes by celebrating the richness of the ecosystem populated by the "metagenome."
© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.

Entities:  

Keywords:  Functional annotation; Metagenomics; Networks; Next-generation sequencing; Pathways; Taxonomy; Visualization

Mesh：

Year:  2021        PMID： 34657989     DOI： 10.1007/s10142-021-00810-y

Source DB:  PubMed          Journal:  Funct Integr Genomics        ISSN： 1438-793X            Impact factor:   3.410


  252 in total

1.  Pathway Activity Profiling (PAPi): from the metabolite profile to the metabolic pathway activity.

Authors:  Raphael B M Aggio; Katya Ruggiero; Silas Granato Villas-Bôas
Journal:  Bioinformatics       Date:  2010-10-06       Impact factor: 6.937

2.  MuffinInfo: HTML5-Based Statistics Extractor from Next-Generation Sequencing Data.

Authors:  Andy S Alic; Ignacio Blanquer
Journal:  J Comput Biol       Date:  2016-09       Impact factor: 1.479

Review 3.  Targeting Dysbiosis for the Treatment of Liver Disease.

Authors:  Gobind Anand; Amir Zarrinpar; Rohit Loomba
Journal:  Semin Liver Dis       Date:  2016-02-12       Impact factor: 6.115

4.  Zseq: An Approach for Preprocessing Next-Generation Sequencing Data.

Authors:  Abedalrhman Alkhateeb; Luis Rueda
Journal:  J Comput Biol       Date:  2017-04-17       Impact factor: 1.479

5.  k-SLAM: accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets.

Authors:  David Ainsworth; Michael J E Sternberg; Come Raczy; Sarah A Butcher
Journal:  Nucleic Acids Res       Date:  2017-02-28       Impact factor: 16.971

6.  Binning metagenomic contigs by coverage and composition.

Authors:  Johannes Alneberg; Brynjar Smári Bjarnason; Ino de Bruijn; Melanie Schirmer; Joshua Quick; Umer Z Ijaz; Leo Lahti; Nicholas J Loman; Anders F Andersson; Christopher Quince
Journal:  Nat Methods       Date:  2014-09-14       Impact factor: 28.547

7.  Scalable metagenomic taxonomy classification using a reference genome database.

Authors:  Sasha K Ames; David A Hysom; Shea N Gardner; G Scott Lloyd; Maya B Gokhale; Jonathan E Allen
Journal:  Bioinformatics       Date:  2013-07-04       Impact factor: 6.937

8.  MetaStorm: A Public Resource for Customizable Metagenomics Annotation.

Authors:  Gustavo Arango-Argoty; Gargi Singh; Lenwood S Heath; Amy Pruden; Weidong Xiao; Liqing Zhang
Journal:  PLoS One       Date:  2016-09-15       Impact factor: 3.240

9.  Reliable Biomarker discovery from Metagenomic data via RegLRSD algorithm.

Authors:  Mustafa Alshawaqfeh; Ahmad Bashaireh; Erchin Serpedin; Jan Suchodolski
Journal:  BMC Bioinformatics       Date:  2017-07-10       Impact factor: 3.169

10.  aRNApipe: a balanced, efficient and distributed pipeline for processing RNA-seq data in high-performance computing environments.

Authors:  Arnald Alonso; Brittany N Lasseigne; Kelly Williams; Josh Nielsen; Ryne C Ramaker; Andrew A Hardigan; Bobbi Johnston; Brian S Roberts; Sara J Cooper; Sara Marsal; Richard M Myers
Journal:  Bioinformatics       Date:  2017-06-01       Impact factor: 6.937
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  1 in total

Review 1.  Detangling the Crosstalk Between Ascaris, Trichuris and Gut Microbiota: What´s Next?

Authors:  Sergio Castañeda; Alberto Paniz-Mondolfi; Juan David Ramírez
Journal:  Front Cell Infect Microbiol       Date:  2022-05-25       Impact factor: 6.073
  1 in total

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