Viruses and Bioinformatics from Virology.uvic.ca
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Viruses and Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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OrfM: A fast open reading frame predictor for metagenomic data

Summary: Finding and translating stretches of DNA lacking stop codons is a task common in the analysis of sequence data. However the computational tools for finding open reading frames are sufficiently slow that they are becoming a bottleneck as the volume of sequence data grows. This computational bottleneck is especially problematic in metagenomics when searching unassembled reads, or screening assembled contigs for genes of interest. Here we present OrfM, a tool to rapidly identify open reading frames (ORFs) in sequence data by applying the Aho-Corasick algorithm to find regions uninterrupted by stop codons. Benchmarking revealed that OrfM finds identical ORFs to similar tools (‘GetOrf’ and ‘Translate’) but is five times faster. While OrfM is sequencing platform-agnostic, it is best suited to large, high quality datasets such as those produced by Illumina sequencers.
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MOCAT2: a metagenomic assembly, annotation and profiling framework

Summary: MOCAT2 is a software pipeline for metagenomic sequence assembly and gene prediction with novel features for taxonomic and functional abundance profiling. The automated generation and efficient annotation of non-redundant reference catalogs by propagating pre-computed assignments from 18 databases covering various functional categories allows for fast and comprehensive functional characterization of metagenomes.
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SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data

Analyzing the functional profile of a microbial community from unannotated shotgun sequencing reads is one of the important goals in metagenomics. Functional profiling has valuable applications in biological research because it identifies the abundances of the functional genes of the organisms present in the original sample, answering the question what they can do. Currently, available tools do not scale well with increasing data volumes, which is important because both the number and lengths of the reads produced by sequencing platforms keep increasing. Here, we introduce SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances. SUPER-FOCUS was tested with over 70 real metagenomes, the results showing that it accurately predicts the subsystems present in the profiled microbial communities, and is up to 1000 times faster than other tools.

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Two Excellent Reviews on Metagenomics « Homolog.us – Bioinformatics

Paper 1: Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies
- Table 1 of this paper compiles the list of many useful programs.

Paper 2:  An evaluation of the accuracy and speed of metagenome analysis tools

- benchmarks a number of analysis tools

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Scooped by Ed Rybicki
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Metagenomic Characterization of Airborne Viral DNA Diversity in the Near-Surface Atmosphere

"Airborne viruses are expected to be ubiquitous in the atmosphere but they still remain poorly understood. This study investigated the temporal and spatial dynamics of airborne viruses and their genotypic characteristics in air samples collected from three distinct land use types (a residential district [RD], a forest [FR], and an industrial complex [IC]) and from rainwater samples freshly precipitated at the RD site (RD-rain). Viral abundance exhibited a seasonal fluctuation in the range between 1.7 × 106 and 4.0 × 107 viruses m−3, which increased from autumn to winter and decreased toward spring, but no significant spatial differences were observed. Temporal variations in viral abundance were inversely correlated with seasonal changes in temperature and absolute humidity. Metagenomic analysis of air viromes amplified by rolling-circle phi29 polymerase-based random hexamer priming indicated the dominance of plant-associated single-stranded DNA (ssDNA) geminivirus-related viruses, followed by animal-infecting circovirus-related sequences, with low numbers of nanoviruses and microphages-related genomes. Particularly, the majority of the geminivirus-related viruses were closely related to ssDNA mycoviruses that infect plant-pathogenic fungi. Phylogenetic analysis based on the replication initiator protein sequence indicated that the airborne ssDNA viruses were distantly related to known ssDNA viruses, suggesting that a high diversity of viruses were newly discovered. This research is the first to report the seasonality of airborne viruses and their genetic diversity, which enhances our understanding of viral ecology in temperate regions."

 

Unbelievably cool - and even more so because they found tonnes of my favourite kinds of genomes, namely, gemini- and circoviruses.

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PLoS ONE: Assessing the Diversity and Specificity of Two Freshwater Viral Communities through Metagenomics

PLoS ONE: Assessing the Diversity and Specificity of Two Freshwater Viral Communities through Metagenomics | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Transitions between saline and fresh waters have been shown to be infrequent for microorganisms. Based on host-specific interactions, the presence of specific clades among hosts suggests the existence of freshwater-specific viral clades.

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DUDes: a top-down taxonomic profiler for metagenomics

Motivation: Species identification and quantification are common tasks in metagenomics and pathogen detection studies. The most recent techniques are built on mapping the sequenced reads against a reference database (e.g. whole genomes, marker genes, proteins) followed by application-dependent analysis steps. Although these methods have been proven to be useful in many scenarios, there is still room for improvement in species and strain level detection, mainly for low abundant organisms.

Results: We propose a new method: DUDes, a reference-based taxonomic profiler that introduces a novel top-down approach to analyze metagenomic Next-generation sequencing (NGS) samples. Rather than predicting an organism presence in the sample based only on relative abundances, DUDes first identifies possible candidates by comparing the strength of the read mapping in each node of the taxonomic tree in an iterative manner. Instead of using the lowest common ancestor we propose a new approach: the deepest uncommon descendent. We showed in experiments that DUDes works for single and multiple organisms and can identify low abundant taxonomic groups with high precision.

Availability and Implementation: DUDes is open source and it is available at http://sf.net/p/dudes
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ViromeScan: a new tool for metagenomic viral community profiling

ViromeScan: a new tool for metagenomic viral community profiling | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
ViromeScan is an innovative metagenomic analysis tool that characterizes the taxonomy of the virome directly from raw data of next-generation sequencing. The tool uses hierarchical databases for eukaryotic viruses to unambiguously assign reads to viral species more accurately and >1000 fold faster than other existing approaches. We validated ViromeScan on synthetic microbial communities and applied it on metagenomic samples of the Human Microbiome Project, providing a sensitive eukaryotic virome profiling of different human body sites.
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Kaiju: Fast and sensitive taxonomic classification for metagenomics

Abstract: The constantly decreasing cost and increasing output of current sequencing technologies enable large scale metagenomic studies of microbial communities from diverse habitats. Therefore, fast and accurate methods for taxonomic classification are needed, which can operate on increasingly larger datasets and reference databases. Recently, several fast metagenomic classifiers have been developed, which are based on comparison of genomic k-mers. However, nucleotide comparison using a fixed k-mer length often lacks the sensitivity to overcome the evolutionary distance between sampled species and genomes in the reference database. Here, we present the novel metagenome classifier Kaiju for fast assignment of reads to taxa. Kaiju finds maximum exact matches on the protein-level using the Borrows-Wheeler transform, and can optionally allow amino acid substitutions in the search using a greedy heuristic. We show in a genome exclusion study that Kaiju can classify more reads with higher sensitivity and similar precision compared to fast k-mer based classifiers, especially in genera that are underrepresented in reference databases. We also demonstrate that Kaiju classifies more than twice as many reads in ten real metagenomes compared to programs based on genomic k-mers. Kaiju can process up to millions of reads per minute, and its memory footprint is below 5 GB of RAM, allowing the analysis on a standard PC. The program is available under the GPL3 license at: github.com/bioinformatics-centre/kaiju

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BMC Bioinformatics | Full text | Metavir 2: new tools for viral metagenome comparison and assembled virome analysis

Metagenomics, based on culture-independent sequencing, is a well-fitted approach to provide insights into the composition, structure and dynamics of environmental viral communities. Following recent advances in sequencing technologies, new challenges arise for existing bioinformatic tools dedicated to viral metagenome (i.e. virome) analysis as (i) the number of viromes is rapidly growing and (ii) large genomic fragments can now be obtained by assembling the huge amount of sequence data generated for each metagenome.

 

The new features of Metavir 2 allow users to explore and analyze viromes composed of raw reads or assembled fragments through a set of adapted tools and a user-friendly interface.

 

http://metavir-meb.univ-bpclermont.fr/

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Metagenomic Analysis of Viruses from Bat Fecal Samples Reveals Many Novel Viruses in Insectivorous Bats in China

Increasing data indicate that bats harbor diverse viruses, some of which cause severe human diseases. In this study, sequence-independent amplification and high-throughput sequencing (Solexa) were applied to the metagenomic analysis of viruses in bat fecal samples collected from 6 locations in China.

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Rescooped by Ed Rybicki from The Microbiology Mine
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Microbial Metagenomics Summer Course 2012 - MSU Metagenomics

Microbial Metagenomics Summer Course 2012 - MSU Metagenomics | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Microbial metagenomics course, June 3 - June 16th, Michigan State University: http://t.co/IXBu9RHO...


Via Elsevier Microbiol*
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