Virology and Bioinformatics from Virology.ca
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Virology and Bioinformatics from Virology.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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Scooped by Cindy
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What Can We Learn from a Metagenomic Analysis of a Georgian Bacteriophage Cocktail?

Phage therapy, a practice widespread in Eastern Europe, has untapped potential in the combat against antibiotic-resistant bacterial infections. However, technology transfer to Western medicine is proving challenging. Bioinformatics analysis could help to facilitate this endeavor.
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MetaQUAST: evaluation of metagenome assemblies

Summary: During the past years we have witnessed the rapid development of new metagenome assembly methods. While there are many benchmark utilities designed for single-genome assemblies, there is no well-recognised evaluation and comparison tool for metagenomic-specific analogues. In this paper we present MetaQUAST, a modification of QUAST, the state-of-the-art tool for genome assembly evaluation based on alignment of contigs to a reference. MetaQUAST addresses such metagenome datasets features as (1) unknown species content by detecting and downloading reference sequences, (2) huge diversity by giving comprehensive reports for multiple genomes, (3) presence of highly relative species by detecting chimeric contigs. We demonstrate MetaQUAST performance by comparing several leading assemblers on one simulated and two real datasets.
 

Availability: http://bioinf.spbau.ru/metaquast

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Fast genome and metagenome distance estimation using MinHash

Given a massive collection of sequences, it is infeasible to perform pairwise alignment for basic tasks like sequence clustering and search. Our new tool, Mash, uses MinHash locality-sensitive hashing to reduce large sequences to a representative sketch and rapidly estimate pairwise distances between genomes or metagenomes...The resulting 93 MB sketch database includes all RefSeq genomes, effectively delineates known species boundaries, reconstructs approximate phylogenies, and can be searched in seconds using assembled genomes or raw sequencing runs from Illumina, Pacific Biosciences, and Oxford Nanopore. For metagenomics, Mash scales to thousands of samples and can replicate Human Microbiome Project and Global Ocean Survey results in a fraction of the time. Other potential applications include any problem where an approximate, global sequence distance is acceptable, e.g. to triage and cluster sequence data, assign species labels to unknown genomes, quickly identify mis-tracked samples, and search massive genomic databases.

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[2013.12.02] Mads Albertsen: Extracting Genomes from Metagenomes

Invited lecture at University of Vienna on extracting genomes from metagenomes.

Via Wei Shen
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Assembly of metagenomes

Lex Nederbragt: "A talk for I gave for the 2011 metagenomics course at the Biological Dept. Univ. Oslo"

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