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MAPseq: improved speed, accuracy and consistency in ribosomal RNA sequence analysis

View ORCID ProfileJoão F Matias Rodrigues, View ORCID ProfileThomas SB Schmidt, Janko Tackmann, View ORCID ProfileChristian von Mering
doi: https://doi.org/10.1101/126953
João F Matias Rodrigues
1Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland.
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  • ORCID record for João F Matias Rodrigues
Thomas SB Schmidt
1Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland.
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Janko Tackmann
1Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland.
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Christian von Mering
1Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland.
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  • ORCID record for Christian von Mering
  • For correspondence: mering@imls.uzh.ch
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Abstract

Metagenomic sequencing has become crucial to studying microbial communities, but meaningful taxonomic analysis and inter-comparison of such data are still hampered by technical limitations, between-study design variability and inconsistencies between taxonomies used. Here we present MAPseq, a framework for reference-based rRNA metagenomic analysis that is up to 30% more accurate (F1/2 score) and up to one hundred times faster than existing solutions, providing in a single run multiple taxonomy classifications and hierarchical OTU mappings, for both amplicon and shotgun sequencing strategies, and for datasets of virtually any size. Availability: Source code and binaries are freely available at http://meringlab.org/software/mapseq/

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted April 12, 2017.
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MAPseq: improved speed, accuracy and consistency in ribosomal RNA sequence analysis
João F Matias Rodrigues, Thomas SB Schmidt, Janko Tackmann, Christian von Mering
bioRxiv 126953; doi: https://doi.org/10.1101/126953
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MAPseq: improved speed, accuracy and consistency in ribosomal RNA sequence analysis
João F Matias Rodrigues, Thomas SB Schmidt, Janko Tackmann, Christian von Mering
bioRxiv 126953; doi: https://doi.org/10.1101/126953

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