Metagenomic sequencing has emerged as a technology of choice for analyzing bacterial populations and discovery of novel organisms and genes. While different groups have developed specialized tools for de novo metagenomic assembly, the problem of assembling complex microbial communities is far from being resolved.
First part of this talk talk will be devoted to our metaSPAdes software, which integrated proven solutions from the SPAdes toolkit with metagenomics-specific techniques. We will highlight key differences between SPAdes and metaSPAdes and advertise recently added (or soon to be released) features, e.g. support of third generation sequencing technologies for hybrid metagenomic assemblies.
In the second part, we will present our novel (yet unpublished) pipeline for improved reconstruction of individual organisms from (time or spatial) metagenomic series. While availability of sequencing data for multiple related samples provides an unprecedented opportunity for the accurate reconstruction of individual microbial community members, widely used approaches demonstrate some major deficiencies and limitations. In an attempt to overcome those, we developed MTS (Metagenomic Time Series) pipeline that integrates state-of-the art differential binning approaches with valuable (and largely underappreciated) ideas from early works on metagenomic series analysis.
