May 18, 2019 Software Open Access

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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    <subfield code="a">&lt;p&gt;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.&lt;/p&gt;

&lt;p&gt;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.&lt;/p&gt;</subfield>
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