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bioRxiv · 10.1101/2020.04.23.057133

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

Puente-Sanchez, F.·Garcia-Garcia, N.·Tamames, J.
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Abstract

BackgroundThe 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. ResultsHere 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 anvio 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. ConclusionsAltogether, 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.

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Puente-Sanchez, F., Garcia-Garcia, N., Tamames, J.. 2020-04-25. SQMtools: automated processing and visual analysis of 'omics data with R and anvi'o. https://doi.org/10.1101/2020.04.23.057133

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