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.
<?xml version='1.0' encoding='utf-8'?> <oai_dc:dc xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd"> <dc:creator>Marcelino, V. R.</dc:creator> <dc:creator>Clausen, P.T.C.L</dc:creator> <dc:creator>Buchmann, J.P.</dc:creator> <dc:creator>Wille, M.</dc:creator> <dc:creator>Iredell, J.R.</dc:creator> <dc:creator>Meyer, W.</dc:creator> <dc:creator>Lund, O.</dc:creator> <dc:creator>Sorrell, T.C.</dc:creator> <dc:creator>Holmes, E.C.</dc:creator> <dc:date>2019-05-18</dc:date> <dc:description>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. 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.</dc:description> <dc:identifier>https://zenodo.org/record/3668497</dc:identifier> <dc:identifier>10.5281/zenodo.3668497</dc:identifier> <dc:identifier>oai:zenodo.org:3668497</dc:identifier> <dc:language>eng</dc:language> <dc:relation>doi:10.1101/641332</dc:relation> <dc:relation>doi:10.5281/zenodo.3668496</dc:relation> <dc:rights>info:eu-repo/semantics/openAccess</dc:rights> <dc:rights>https://creativecommons.org/licenses/by/4.0/legalcode</dc:rights> <dc:subject>metagenomics</dc:subject> <dc:subject>microbiome</dc:subject> <dc:title>CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data</dc:title> <dc:type>info:eu-repo/semantics/other</dc:type> <dc:type>software</dc:type> </oai_dc:dc>