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SQMtools: automated processing and visual analysis of 'omics data with R and anvi'o.


ABSTRACT: BACKGROUND:The dramatic decrease in sequencing costs over the last decade has boosted the adoption of high-throughput sequencing applications as a standard tool for the analysis of environmental microbial communities. Nowadays even small research groups can easily obtain raw sequencing data. After that, however, non-specialists are faced with the double challenge of choosing among an ever-increasing array of analysis methodologies, and navigating the vast amounts of results returned by these approaches. RESULTS:Here we present a workflow that relies on the SqueezeMeta software for the automated processing of raw reads into annotated contigs and reconstructed genomes (bins). A set of custom scripts seamlessly integrates the output into the anvi'o analysis platform, allowing filtering and visual exploration of the results. Furthermore, we provide a software package with utility functions to expose the SqueezeMeta results to the R analysis environment. CONCLUSIONS:Altogether, our workflow allows non-expert users to go from raw sequencing reads to custom plots with only a few powerful, flexible and well-documented commands.

SUBMITTER: Puente-Sanchez F 

PROVIDER: S-EPMC7430844 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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SQMtools: automated processing and visual analysis of 'omics data with R and anvi'o.

Puente-Sánchez Fernando F   García-García Natalia N   Tamames Javier J  

BMC bioinformatics 20200814 1


<h4>Background</h4>The dramatic decrease in sequencing costs over the last decade has boosted the adoption of high-throughput sequencing applications as a standard tool for the analysis of environmental microbial communities. Nowadays even small research groups can easily obtain raw sequencing data. After that, however, non-specialists are faced with the double challenge of choosing among an ever-increasing array of analysis methodologies, and navigating the vast amounts of results returned by t  ...[more]

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