Biology subjects

Garcia-Garcia, N.

Publications and source records attributed to Garcia-Garcia, N..

3 recordsLinked to original sources

bioRxiv2021

M&Ms: A software for building realistic Microbial Mock communities

MotivationAdvances in sequencing technologies have triggered the development of many bioinformatic tools aimed to analyze these data. As these tools need to be tested, it is important to simulate datasets that resemble realistic conditions. Although there is a large amount of software dedicated to produce reads from in silico microbial communities, often the simulated data diverge widely from real situations. ResultsHere, we introduce M&Ms, a user-friendly open-source bioinformatic tool to produce realistic amplicon datasets from reference sequences, based on pragmatic ecological parameters. This tool creates sequence libraries for in silico microbial communities with user-controlled richness, evenness, microdiversity, and source environment. M&Ms allows the user to generate simple to complex read datasets based on real parameters that can be used in developing bioinformatic software or in benchmarking current tools. M&Ms also provides additional figures and files with extensive details on how each synthetic community is composed, so that users can make informed choices when designing their benchmarking pipelines. AvailabilityThe source code of M&Ms is freely available from https://github.com/ggnatalia/MMs Contactngarcia@cnb.csic.es

bioinformatics↗

bioRxiv2020

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

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.

bioinformatics↗

bioRxiv2019

Intra-species diversity ensures the maintenance of functional microbial communities under changing environmental conditions

Intra-species diversity comprises different ecotypes within the same species. These are assumed to provide stability in time and space to those species. However, the role that microdiversity plays in the stability of whole microbial communities remains underexplored. Understanding the drivers of microbial community stability is necessary to predict community response to future disturbances. Here, we analyzed 16S rRNA gene amplicons from eight different temperate bog lakes at OTU-97% and amplicon sequence variant (ASV) levels, and we found ecotypes within the same species with different distribution patterns in space and time. We observed that these ecotypes are adapted to different values of environmental factors such as water temperature and oxygen concentration. Our results showed that the existence of several ASVs within a species favored its persistence across changing environmental conditions. We propose that microdiversity aids the stability of microbial communities in the face of fluctuations in environmental factors.

ecology↗