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

Marcelino, V. R.; Clausen, P.T.C.L; Buchmann, J.P.; Wille, M.; Iredell, J.R.; Meyer, W.; Lund, O.; Sorrell, T.C.; Holmes, E.C.


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    "description": "<p>CCMetagen is a software to identify taxa from metagenome data. This repository contains CCMetagen version 1.0.0, which was benchmarked with other software in the original CCMetagen publication.</p>\n\n<p>High-throughput sequencing of DNA and RNA from environmental and host-associated samples (metagenomics and metatranscriptomics) is a powerful tool to assess which organisms are present in a sample. Taxonomic identification software usually align individual short sequence reads to a reference database, sometimes containing taxa with complete genomes only. This is a challenging task given that different species can share identical sequence regions and complete genome sequences are only available for a fraction of organisms. A recently developed approach to map sequence reads to reference databases involves weighing all high scoring read-mappings to the data base as a whole to produce better-informed alignments. We used this novel concept in read mapping to develop a highly accurate metagenomic classification pipeline named CCMetagen. Our 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.</p>", 
    "language": "eng", 
    "title": "CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data", 
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    "publication_date": "2019-05-18", 
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        "affiliation": "The University of Sydney", 
        "name": "Marcelino, V. R."
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        "affiliation": "Technical University of Denmark", 
        "name": "Clausen, P.T.C.L"
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        "name": "Lund, O."
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        "affiliation": "The University of Sydney", 
        "name": "Sorrell, T.C."
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