MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs.

BACKGROUND: Current methods used for annotating metagenomics shotgun sequencing (MGS) data rely on a computationally intensive and low-stringency approach of mapping each read to a generic database of proteins or reference microbial genomes. RESULTS: We developed MGS-Fast, an analysis approach for shotgun whole-genome metagenomic data utilizing Bowtie2 DNA-DNA alignment of reads that is an alternative to using the integrated catalog of reference genes database of well-annotated genes compiled from human microbiome data. This method is rapid and provides high-stringency matches (>90% DNA sequence identity) of the metagenomics reads to genes with annotated functions. We demonstrate the use of this method with data from a study of liver disease and synthetic reads, and Human Microbiome Project shotgun data, to detect differentially abundant Kyoto Encyclopedia of Genes and Genomes gene functions in these experiments. This rapid annotation method is freely available as a Galaxy workflow within a Docker image. CONCLUSIONS: MGS-Fast can confidently transfer functional annotations from gene databases to metagenomic reads, with speed and accuracy.

miCloud: A Plug-n-Play, Extensible, On-Premises Bioinformatics Cloud for Seamless Execution of Complex Next-Generation Sequencing Data Analysis Pipelines.

The availability of low-cost small-factor sequencers, such as the Illumina MiSeq, MiniSeq, or iSeq, have paved the way for democratizing genomics sequencing, providing researchers in minority universities with access to the technology that was previously only affordable by institutions with large core facilities. However, these instruments are not bundled with software for performing bioinformatics data analysis, and the data analysis can be the main bottleneck for independent laboratories or even small clinical facilities that consider adopting genomic sequencing for medical applications. To address this issue, we have developed miCloud, a bioinformatics platform that enables genomic data analysis through a fully featured data analysis cloud, which seamlessly integrates with genome sequencers over the local network. The miCloud can be easily deployed without any prior bioinformatics expertise on any computing environment, from a laboratory computer workstation to a university computer cluster. Our platform not only provides access to a set of preconfigured RNA-Seq and CHIP-Seq bioinformatics pipelines, but also enables users to develop or install new preconfigured tools from the large selection available on open-source online Docker container repositories. The miCloud built-in analysis pipelines are also integrated with the Visual Omics Explorer framework (Kim et al., 2016), which provides rich interactive visualizations and publication-ready graphics from the next-generation sequencing data. Ultimately, the miCloud demonstrates a bioinformatics approach that can be adopted in the field for standardizing genomic data analysis, similarly to the way molecular biology sample preparation kits have standardized laboratory operations.

Bio-Docklets: virtualization containers for single-step execution of NGS pipelines.

Processing of next-generation sequencing (NGS) data requires significant technical skills, involving installation, configuration, and execution of bioinformatics data pipelines, in addition to specialized postanalysis visualization and data mining software. In order to address some of these challenges, developers have leveraged virtualization containers toward seamless deployment of preconfigured bioinformatics software and pipelines on any computational platform. We present an approach for abstracting the complex data operations of multistep, bioinformatics pipelines for NGS data analysis. As examples, we have deployed 2 pipelines for RNA sequencing and chromatin immunoprecipitation sequencing, preconfigured within Docker virtualization containers we call Bio-Docklets. Each Bio-Docklet exposes a single data input and output endpoint and from a user perspective, running the pipelines as simply as running a single bioinformatics tool. This is achieved using a "meta-script" that automatically starts the Bio-Docklets and controls the pipeline execution through the BioBlend software library and the Galaxy Application Programming Interface. The pipeline output is postprocessed by integration with the Visual Omics Explorer framework, providing interactive data visualizations that users can access through a web browser. Our goal is to enable easy access to NGS data analysis pipelines for nonbioinformatics experts on any computing environment, whether a laboratory workstation, university computer cluster, or a cloud service provider. Beyond end users, the Bio-Docklets also enables developers to programmatically deploy and run a large number of pipeline instances for concurrent analysis of multiple datasets.

Visual Omics Explorer (VOE): a cross-platform portal for interactive data visualization.

MOTIVATION: Given the abundance of genome sequencing and omics data, an opprtunity and challenge in bioinformatics relates to data mining and visualization. The majority of current bioinformatics visualizations are implemented either as multi-tier web server applications that require significant maintenance effort, or as client software that presumes technical expertise for installation. Here we present the Visual Omics Explorer (VOE), a cross-platform data visualization portal that is implemented using only HTML and Javascript code. VOE is a standalone software that can be loaded offline on the web browser from a local copy of the code, or over the internet without any dependency other than distributing the code through a file sharing service. VOE can interactively display genomics, transcriptomics, epigenomics and metagenomics data stored either locally or retrieved from cloud storage services, and runs on both desktop computers and mobile devices. AVAILABILITY AND IMPLEMENTATION: VOE is accessible at http://bcil.github.io/VOE/ CONTACT: agbiotec@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.