Journal
BMC BIOINFORMATICS
Volume 21, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/s12859-020-03703-2
Keywords
Metagenomics; Metatranscriptomics; Microbial ecology; Automatic; Pipeline; Visualization
Categories
Funding
- Spanish Ministry of Economy of Competitiveness [CTM2016-80095-C2-1-R, PID2019-110011RB-C31]
- Spanish Ministry of Science and Innovation [IJC2018-035180-I, SEV-2013-0347-17-2]
- CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI)
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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.
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