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\begin{document}

\title{In-situ metagenomics: A platform for on-field rapid sequencing and
analysis of metagenomes in less than one day}



\author[1]{Javier Tamames}%
\author[1]{Diego Jiménez-Lalana}%
\author[1]{Alvaro Redondo}%
\author[2]{Sandra Martínez-García}%
\author[3]{Asunción de los Ríos}%
\affil[1]{Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC)}%
\affil[2]{Universidade de Vigo}%
\affil[3]{Museo Nacional de Ciencias Naturales}%


\vspace{-1em}



  
  \date{May 26, 2024}


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\begin{abstract}
We present a complete portable pipeline for sequencing and analysis of
environmental metagenomes in less than a day. This unprecedented
development was possible due to the conjunction of state-of-the art
experimental and computational advances: a portable laboratory suitable
for DNA extraction and sequencing with nanopore technology.The powerful
metagenomic analysis pipeline SqueezeMeta, capable to provide a complete
analysis in a few hours and using scarce computational resources.
Finally, tools for the automatic inspection of the results via a
graphical user interface, that can be coupled to a web server to allow
remote visualization of data (SQMtools and SQMxplore). We tested the
feasibility of our approach in the sequencing of the microbiota
associated to volcanic rocks in La Palma, Canary Islands. Also, we did a
two-day sampling campaign of marine waters in which the results obtained
the first day guided the experimental design of the second day. We
demonstrate that it is possible to generate metagenomic information in
less than one day, making it feasible to obtain taxonomic and functional
profiles fast and efficiently, even in field conditions. This capacity
can be used in the further to perform real-time functional and taxonomic
profiling of microbial communities in remote areas%
\end{abstract}%



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