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Bioinformatics in Microbiota

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Front. Microbiol. | doi: 10.3389/fmicb.2018.03349

SqueezeM, a highly portable, fully automatic metagenomic analysis pipeline

  • 1Centro Nacional de Biotecnología (CNB), Spain

The improvement of sequencing technologies has facilitated generalization of metagenomic sequencing, which has become a standard procedure for analyzing the structure and functionality of microbiomes. Bioinformatic analysis of sequencing results poses a challenge because this involves many different complex steps.

SqueezeMeta is a fully automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support that enables co-assembly of related metagenomes and retrieval of individual genomes via binning procedures. SqueezeMeta features several unique characteristics: co-assembly procedure or co-assembly of unlimited number of metagenomes via merging of individual assembled metagenomes, both with read mapping for estimation of the abundances of genes in each metagenome. It also includes binning and bin checking for retrieving individual genomes. Internal checks for the assembly and binning steps provide information about the consistency of contigs and bins. Moreover, results are stored in a mySQL database, where they can be easily exported and shared, and can be inspected anywhere using a flexible web interface that allows simple creation of complex queries.

We illustrate the potential of SqueezeMeta by analyzing 32 gut metagenomes in a fully automatic way, enabling retrieval of several million genes and several hundreds of genomic bins.

One of the motivations in the development of SqueezeMeta was producing a software capable of running in small desktop computers and thus amenable to all users and settings. We were also able to co-assemble two of these metagenomes and complete the full analysis in less than one day using a simple laptop computer. This reveals the capacity of SqueezeMeta to run without high-performance computing infrastructure.

SqueezeMeta is a complete system covering all steps in the analysis of metagenomes and metatranscriptomes; it is capable of working even in scarce computational resources. It is therefore adequate for in-situ, real time analysis of metagenomes produced by nanopore sequencing. SqueezeMeta can be downloaded from

Keywords: Software, Metagenomics, RNAseq, metatranscriptomics, Binning, MinION

Received: 19 Sep 2018; Accepted: 31 Dec 2018.

Edited by:

Qi Zhao, Liaoning University, China

Reviewed by:

Alfredo Ferro, Università degli Studi di Catania, Italy
Yu-Wei Wu, Graduate Institute of Biomedical Informatics, Taipei Medical University, Taiwan  

Copyright: © 2018 Tamames and Puente-Sanchez. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Javier Tamames, Centro Nacional de Biotecnología (CNB), Madrid, Spain,