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DIAMOND+MEGAN: Fast and Easy Taxonomic and Functional Analysis of Short and Long Microbiome Sequences
Author(s) -
Bağcı Caner,
Patz Sascha,
Huson Daniel H.
Publication year - 2021
Publication title -
current protocols
Language(s) - English
Resource type - Journals
ISSN - 2691-1299
DOI - 10.1002/cpz1.59
Subject(s) - microbiome , preprocessor , biological classification , computational biology , contig , protocol (science) , metagenomics , computer science , taxonomic rank , biology , bioinformatics , data mining , pattern recognition (psychology) , artificial intelligence , evolutionary biology , genetics , taxon , ecology , genome , gene , medicine , alternative medicine , pathology
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. This article was corrected on 20 July 2022. See the end of the full text for details. 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