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Struo: a pipeline for building custom databases for common metagenome profilers

Jacobo de la Cuesta-Zuluaga, Ruth E. Ley, View ORCID ProfileNicholas D. Youngblut
doi: https://doi.org/10.1101/774372
Jacobo de la Cuesta-Zuluaga
1Department of Microbiome Science. Max Planck Institute for Developmental Biology. Tübingen, Germany
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  • For correspondence: nyoungblut@tuebingen.mpg.de
Ruth E. Ley
1Department of Microbiome Science. Max Planck Institute for Developmental Biology. Tübingen, Germany
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Nicholas D. Youngblut
1Department of Microbiome Science. Max Planck Institute for Developmental Biology. Tübingen, Germany
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  • ORCID record for Nicholas D. Youngblut
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Abstract

Summary Taxonomic and functional information from microbial communities can be efficiently obtained by metagenome profiling, which requires databases of genes and genomes to which sequence reads are mapped. However, the databases that accompany metagenome profilers are not updated at a pace that matches the increase in available microbial genomes. To address this, we developed Struo, a modular pipeline that automatizes the acquisition of genomes from public repositories and the construction of custom databases for multiple metagenome profilers. The use of custom databases that broadly represent the known microbial diversity by incorporating novel genomes results in a substantial increase in mappability of reads in synthetic and real metagenome datasets.

Availability and implementation Source code available for download at https://github.com/leylabmpi/Struo. Custom GTDB databases available at http://ftp.tue.mpg.de/ebio/projects/struo/

Contact nicholas.youngblut{at}tuebingen.mpg.de

Footnotes

  • https://github.com/leylabmpi/Struo

  • http://ftp.tue.mpg.de/ebio/projects/struo/

Copyright 
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-ND 4.0 International license.
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Posted September 23, 2019.
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Struo: a pipeline for building custom databases for common metagenome profilers
Jacobo de la Cuesta-Zuluaga, Ruth E. Ley, Nicholas D. Youngblut
bioRxiv 774372; doi: https://doi.org/10.1101/774372
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Struo: a pipeline for building custom databases for common metagenome profilers
Jacobo de la Cuesta-Zuluaga, Ruth E. Ley, Nicholas D. Youngblut
bioRxiv 774372; doi: https://doi.org/10.1101/774372

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