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description Publicationkeyboard_double_arrow_right Other literature type 2020Publisher:figshare Funded by:ARC | Australian Laureate Fello..., EC | COMPARE, NHMRC | Protecting the public fro...ARC| Australian Laureate Fellowships - Grant ID: FL170100022 ,EC| COMPARE ,NHMRC| Protecting the public from emerging infectious diseasesAuthors: Marcelino, Vanessa R.; Clausen, Philip T. L. C.; Buchmann, Jan P.; Wille, Michelle; +5 AuthorsMarcelino, Vanessa R.; Clausen, Philip T. L. C.; Buchmann, Jan P.; Wille, Michelle; Iredell, Jonathan R.; Meyer, Wieland; Lund, Ole; Sorrell, Tania C.; Holmes, Edward C.;Additional file 3: Supplementary Materials and Methods.
add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.6084/m9.figshare.12211688&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen 0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.6084/m9.figshare.12211688&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Other literature type 2020Publisher:figshare Funded by:EC | COMPARE, NHMRC | Protecting the public fro..., ARC | Australian Laureate Fello...EC| COMPARE ,NHMRC| Protecting the public from emerging infectious diseases ,ARC| Australian Laureate Fellowships - Grant ID: FL170100022Authors: Marcelino, Vanessa R.; Clausen, Philip T. L. C.; Buchmann, Jan P.; Wille, Michelle; +5 AuthorsMarcelino, Vanessa R.; Clausen, Philip T. L. C.; Buchmann, Jan P.; Wille, Michelle; Iredell, Jonathan R.; Meyer, Wieland; Lund, Ole; Sorrell, Tania C.; Holmes, Edward C.;Additional file 1: Figure S1. Precision of the different methods, using three reference databases. Figure S2: Recall of fungal taxa from a metagenome and a metatranscriptome test dataset.
add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.6084/m9.figshare.12211673.v1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen 0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.6084/m9.figshare.12211673.v1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Other literature type 2020Publisher:figshare Funded by:EC | COMPARE, NHMRC | Protecting the public fro..., ARC | Australian Laureate Fello...EC| COMPARE ,NHMRC| Protecting the public from emerging infectious diseases ,ARC| Australian Laureate Fellowships - Grant ID: FL170100022Authors: Marcelino, Vanessa R.; Clausen, Philip T. L. C.; Buchmann, Jan P.; Wille, Michelle; +5 AuthorsMarcelino, Vanessa R.; Clausen, Philip T. L. C.; Buchmann, Jan P.; Wille, Michelle; Iredell, Jonathan R.; Meyer, Wieland; Lund, Ole; Sorrell, Tania C.; Holmes, Edward C.;Additional file 9: Review history.
add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.6084/m9.figshare.12211724&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen 0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.6084/m9.figshare.12211724&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2019 DenmarkPublisher:Cold Spring Harbor Laboratory Funded by:ARC | Australian Laureate Fello..., EC | COMPARE, NHMRC | Protecting the public fro...ARC| Australian Laureate Fellowships - Grant ID: FL170100022 ,EC| COMPARE ,NHMRC| Protecting the public from emerging infectious diseasesAuthors: Vanessa R. Marcelino; Philip Thomas Lanken Conradsen Clausen; Jan P. Buchmann; Michelle Wille; +5 AuthorsVanessa R. Marcelino; Philip Thomas Lanken Conradsen Clausen; Jan P. Buchmann; Michelle Wille; Jonathan R. Iredell; Wieland Meyer; Ole Lund; Tania C. Sorrell; Edward C. Holmes;AbstractHigh-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. Using simulated fungal and bacterial metagenomes, we demonstrate that CCMetagen substantially outperforms other commonly used metagenome classifiers, attaining a 3 – 1580 fold increase in precision and a 2 – 922 fold increase in F1 scores for species-level classifications when compared to Kraken2, Centrifuge and KrakenUniq. CCMetagen is sufficiently fast and memory efficient to use the entire NCBI nucleotide collection (nt) as reference, enabling the assessment of species with incomplete genome sequence data from all biological kingdoms. Our pipeline efficiently produced a comprehensive overview of the microbiome of two biological data sets, including both eukaryotes and prokaryotes. CCMetagen is user-friendly and the results can be easily integrated into microbial community analysis software for streamlined and automated microbiome studies.
bioRxiv arrow_drop_down bioRxivPreprint . 2019Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7189439Data sources: PubMed CentralOnline Research Database In TechnologyArticle . 2020Data sources: Online Research Database In Technologyadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/641332&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 92 citations 92 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert bioRxiv arrow_drop_down bioRxivPreprint . 2019Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7189439Data sources: PubMed CentralOnline Research Database In TechnologyArticle . 2020Data sources: Online Research Database In Technologyadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/641332&type=result"></script>'); --> </script>
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description Publicationkeyboard_double_arrow_right Other literature type 2020Publisher:figshare Funded by:ARC | Australian Laureate Fello..., EC | COMPARE, NHMRC | Protecting the public fro...ARC| Australian Laureate Fellowships - Grant ID: FL170100022 ,EC| COMPARE ,NHMRC| Protecting the public from emerging infectious diseasesAuthors: Marcelino, Vanessa R.; Clausen, Philip T. L. C.; Buchmann, Jan P.; Wille, Michelle; +5 AuthorsMarcelino, Vanessa R.; Clausen, Philip T. L. C.; Buchmann, Jan P.; Wille, Michelle; Iredell, Jonathan R.; Meyer, Wieland; Lund, Ole; Sorrell, Tania C.; Holmes, Edward C.;Additional file 3: Supplementary Materials and Methods.
add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.6084/m9.figshare.12211688&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen 0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.6084/m9.figshare.12211688&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Other literature type 2020Publisher:figshare Funded by:EC | COMPARE, NHMRC | Protecting the public fro..., ARC | Australian Laureate Fello...EC| COMPARE ,NHMRC| Protecting the public from emerging infectious diseases ,ARC| Australian Laureate Fellowships - Grant ID: FL170100022Authors: Marcelino, Vanessa R.; Clausen, Philip T. L. C.; Buchmann, Jan P.; Wille, Michelle; +5 AuthorsMarcelino, Vanessa R.; Clausen, Philip T. L. C.; Buchmann, Jan P.; Wille, Michelle; Iredell, Jonathan R.; Meyer, Wieland; Lund, Ole; Sorrell, Tania C.; Holmes, Edward C.;Additional file 1: Figure S1. Precision of the different methods, using three reference databases. Figure S2: Recall of fungal taxa from a metagenome and a metatranscriptome test dataset.
add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.6084/m9.figshare.12211673.v1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen 0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.6084/m9.figshare.12211673.v1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Other literature type 2020Publisher:figshare Funded by:EC | COMPARE, NHMRC | Protecting the public fro..., ARC | Australian Laureate Fello...EC| COMPARE ,NHMRC| Protecting the public from emerging infectious diseases ,ARC| Australian Laureate Fellowships - Grant ID: FL170100022Authors: Marcelino, Vanessa R.; Clausen, Philip T. L. C.; Buchmann, Jan P.; Wille, Michelle; +5 AuthorsMarcelino, Vanessa R.; Clausen, Philip T. L. C.; Buchmann, Jan P.; Wille, Michelle; Iredell, Jonathan R.; Meyer, Wieland; Lund, Ole; Sorrell, Tania C.; Holmes, Edward C.;Additional file 9: Review history.
add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.6084/m9.figshare.12211724&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen 0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.6084/m9.figshare.12211724&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2019 DenmarkPublisher:Cold Spring Harbor Laboratory Funded by:ARC | Australian Laureate Fello..., EC | COMPARE, NHMRC | Protecting the public fro...ARC| Australian Laureate Fellowships - Grant ID: FL170100022 ,EC| COMPARE ,NHMRC| Protecting the public from emerging infectious diseasesAuthors: Vanessa R. Marcelino; Philip Thomas Lanken Conradsen Clausen; Jan P. Buchmann; Michelle Wille; +5 AuthorsVanessa R. Marcelino; Philip Thomas Lanken Conradsen Clausen; Jan P. Buchmann; Michelle Wille; Jonathan R. Iredell; Wieland Meyer; Ole Lund; Tania C. Sorrell; Edward C. Holmes;AbstractHigh-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. Using simulated fungal and bacterial metagenomes, we demonstrate that CCMetagen substantially outperforms other commonly used metagenome classifiers, attaining a 3 – 1580 fold increase in precision and a 2 – 922 fold increase in F1 scores for species-level classifications when compared to Kraken2, Centrifuge and KrakenUniq. CCMetagen is sufficiently fast and memory efficient to use the entire NCBI nucleotide collection (nt) as reference, enabling the assessment of species with incomplete genome sequence data from all biological kingdoms. Our pipeline efficiently produced a comprehensive overview of the microbiome of two biological data sets, including both eukaryotes and prokaryotes. CCMetagen is user-friendly and the results can be easily integrated into microbial community analysis software for streamlined and automated microbiome studies.
bioRxiv arrow_drop_down bioRxivPreprint . 2019Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7189439Data sources: PubMed CentralOnline Research Database In TechnologyArticle . 2020Data sources: Online Research Database In Technologyadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/641332&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 92 citations 92 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert bioRxiv arrow_drop_down bioRxivPreprint . 2019Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7189439Data sources: PubMed CentralOnline Research Database In TechnologyArticle . 2020Data sources: Online Research Database In Technologyadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/641332&type=result"></script>'); --> </script>
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