CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data

CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data

Abstract There is an increasing demand for accurate and fast metagenome classifiers that can not only identify bacteria, but all members of a microbial community. We used a recently developed concept in read mapping to develop a highly accurate metagenomic classification pipeline named CCMetagen. Th...

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Bibliographic Details
Main Authors: Vanessa R. Marcelino, Philip T. L. C. Clausen, Jan P. Buchmann, Michelle Wille, Jonathan R. Iredell, Wieland Meyer, Ole Lund, Tania C. Sorrell, Edward C. Holmes
Format: Article
Language:English
Published: BMC 2020-04-01
Series:Genome Biology
Subjects:
Microbiome
Metagenomic classifier
ConClave sorting
Fungi
Online Access:http://link.springer.com/article/10.1186/s13059-020-02014-2
Description
Summary:Abstract There is an increasing demand for accurate and fast metagenome classifiers that can not only identify bacteria, but all members of a microbial community. We used a recently developed concept in read mapping to develop a highly accurate metagenomic classification pipeline named CCMetagen. The pipeline substantially outperforms other commonly used software in identifying bacteria and fungi and can efficiently use the entire NCBI nucleotide collection as a reference to detect species with incomplete genome data from all biological kingdoms. CCMetagen is user-friendly, and the results can be easily integrated into microbial community analysis software for streamlined and automated microbiome studies.
ISSN:1474-760X

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