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


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Article Info

DATE

2020-04-28

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

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. More... »

PAGES

103

References to SciGraph publications

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  • 2012-06-10. Metagenomic microbial community profiling using unique clade-specific marker genes in NATURE METHODS
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  • 2010-07-09. ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases in BMC MICROBIOLOGY
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  • 2015-03-25. CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers in BMC GENOMICS
  • 2014-03-03. Kraken: ultrafast metagenomic sequence classification using exact alignments in GENOME BIOLOGY
  • 2019-11-28. Improved metagenomic analysis with Kraken 2 in GENOME BIOLOGY
  • 2018-10-30. RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification in GENOME BIOLOGY
  • 2017-10-07. Yeasts in Birds in YEASTS IN NATURAL ECOSYSTEMS: DIVERSITY
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  • 2011-09-30. Interactive metagenomic visualization in a Web browser in BMC BIOINFORMATICS
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  • 2019-04-08. Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes in BMC BIOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s13059-020-02014-2

    DOI

    http://dx.doi.org/10.1186/s13059-020-02014-2

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/32345331


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