Literature DB >> 33656283

DIAMOND+MEGAN: Fast and Easy Taxonomic and Functional Analysis of Short and Long Microbiome Sequences.

Caner Bağcı1, Sascha Patz1, Daniel H Huson1.   

Abstract

One main approach to computational analysis of microbiome sequences is to first align against a reference database of annotated protein sequences (NCBI-nr) and then perform taxonomic and functional binning of the sequences based on the resulting alignments. For both short and long reads (or assembled contigs), alignment is performed using DIAMOND, whereas taxonomic and functional binning, followed by inter- active exploration and analysis, is performed using MEGAN. We provide two step-by-step descriptions of this approach:
© 2021 The Authors. Basic Protocol 1: Taxonomic and functional analysis of short read microbiome sequences Support Protocol 1: Preprocessing Basic Protocol 2: taxonomic and functional analysis of assembled long read microbiome sequences Support Protocol 2: Taxonomic binning and CheckM. © 2021 The Authors.

Entities:  

Keywords:  functional binning; metagenome assembled genomes; microbiome sequencing; protein alignment; software; taxonomic binning

Mesh：

Substances：

Year:  2021        PMID： 33656283     DOI： 10.1002/cpz1.59

Source DB:  PubMed          Journal:  Curr Protoc        ISSN： 2691-1299


  7 in total

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Journal:  Sci Rep       Date:  2022-05-24       Impact factor: 4.996

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Authors:  Hao Lin; Qingqing Guo; Zhiyong Wen; Songlin Tan; Jie Chen; Lijian Lin; Pengcheng Chen; Jianquan He; Jianbo Wen; Ye Chen
Journal:  Microb Cell Fact       Date:  2021-12-28       Impact factor: 5.328

3.  Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis.

Authors:  Anupam Gautam; Hendrik Felderhoff; Caner Bağci; Daniel H Huson
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4.  BugSplit enables genome-resolved metagenomics through highly accurate taxonomic binning of metagenomic assemblies.

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5.  Integration of the Human Gut Microbiome and Serum Metabolome Reveals Novel Biological Factors Involved in the Regulation of Bone Mineral Density.

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Journal:  Microbiome       Date:  2022-08-15       Impact factor: 16.837

7.  Whokaryote: distinguishing eukaryotic and prokaryotic contigs in metagenomes based on gene structure.

Authors:  Lotte J U Pronk; Marnix H Medema
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  7 in total

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