Plasmids are stably maintained extra-chromosomal genetic elements that replicate independently from the host cell's chromosomes. Although plasmids harbor biomedically important genes, (such as genes ...involved in virulence and antibiotics resistance), there is a shortage of specialized software tools for extracting and assembling plasmid data from whole genome sequencing projects.
We present the plasmidSPAdes algorithm and software tool for assembling plasmids from whole genome sequencing data and benchmark its performance on a diverse set of bacterial genomes.
plasmidSPAdes is publicly available at http://spades.bioinf.spbau.ru/plasmidSPAdes/ CONTACT: d.antipov@spbu.ruSupplementary information: Supplementary data are available at Bioinformatics online.
Although plasmids are important for bacterial survival and adaptation, plasmid detection and assembly from genomic, let alone metagenomic, samples remain challenging. The recently developed ...plasmidSPAdes assembler addressed some of these challenges in the case of isolate genomes but stopped short of detecting plasmids in metagenomic assemblies, an untapped source of yet to be discovered plasmids. We present the metaplasmidSPAdes tool for plasmid assembly in metagenomic data sets that reduced the false positive rate of plasmid detection compared with the state-of-the-art approaches. We assembled plasmids in diverse data sets and have shown that thousands of plasmids remained below the radar in already completed genomic and metagenomic studies. Our analysis revealed the extreme variability of plasmids and has led to the discovery of many novel plasmids (including many plasmids carrying antibiotic-resistance genes) without significant similarities to currently known ones.
Abstract
Motivation
Although the set of currently known viruses has been steadily expanding, only a tiny fraction of the Earth’s virome has been sequenced so far. Shotgun metagenomic sequencing ...provides an opportunity to reveal novel viruses but faces the computational challenge of identifying viral genomes that are often difficult to detect in metagenomic assemblies.
Results
We describe a MetaviralSPAdes tool for identifying viral genomes in metagenomic assembly graphs that is based on analyzing variations in the coverage depth between viruses and bacterial chromosomes. We benchmarked MetaviralSPAdes on diverse metagenomic datasets, verified our predictions using a set of virus-specific Hidden Markov Models and demonstrated that it improves on the state-of-the-art viral identification pipelines.
Availability and implementation
Metaviral
SPAdes includes ViralAssembly, ViralVerify and ViralComplete modules that are available as standalone packages: https://github.com/ablab/spades/tree/metaviral_publication, https://github.com/ablab/viralVerify/ and https://github.com/ablab/viralComplete/.
Contact
d.antipov@spbu.ru
Supplementary information
Supplementary data are available at Bioinformatics online.
Abstract
Motivation
Recent advancements in long-read RNA sequencing have enabled the examination of full-length isoforms, previously uncaptured by short-read sequencing methods. An alternative ...powerful method for studying isoforms is through the use of barcoded short-read RNA reads, for which a barcode indicates whether two short-reads arise from the same molecule or not. Such techniques included the 10x Genomics linked-read based SParse Isoform Sequencing (SPIso-seq), as well as Loop-Seq, or Tell-Seq. Some applications, such as novel-isoform discovery, require very high coverage. Obtaining high coverage using long reads can be difficult, making barcoded RNA-seq data a valuable alternative for this task. However, most annotation pipelines are not able to work with a set of short reads instead of a single transcript, also not able to work with coverage gaps within a molecule if any. In order to overcome this challenge, we present an RNA-seq assembler that allows the determination of the expressed isoform per barcode.
Results
In this article, we present cloudrnaSPAdes, a tool for assembling full-length isoforms from barcoded RNA-seq linked-read data in a reference-free fashion. Evaluating it on simulated and real human data, we found that cloudrnaSPAdes accurately assembles isoforms, even for genes with high isoform diversity.
Availability and implementation
cloudrnaSPAdes is a feature release of a SPAdes assembler and version used for this article is available at https://github.com/1dayac/cloudrnaSPAdes-release.
Enterotypes of the human gut microbiome have been proposed to be a powerful prognostic tool to evaluate the correlation between lifestyle, nutrition, and disease. However, the number of enterotypes ...suggested in the literature ranged from two to four. The growth of available metagenome data and the use of exact, non-linear methods of data analysis challenges the very concept of clusters in the multidimensional space of bacterial microbiomes. Using several published human gut microbiome datasets of variable 16S rRNA regions, we demonstrate the presence of a lower-dimensional structure in the microbiome space, with high-dimensional data concentrated near a low-dimensional non-linear submanifold, but the absence of distinct and stable clusters that could represent enterotypes. This observation is robust with regard to diverse combinations of dimensionality reduction techniques and clustering algorithms.
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