An article published in BMCGenomics presents Wochenende: A whole genome sequencing alignment pipeline that can identify species of all kingdoms of life using both short and long reads and automatically combine multiple available modules.
outlines the overall flow of information through the Wochenende pipeline including all modular steps and tools. Further modules allow visualization of read distributions across the genome, as well as data integration and plotting of pipeline results. The pipeline is simple to run, robust and highly automated as a step-by-step for installation and running is provided. A global JSON config file contains all relevant setup, options and paths to reference genomes.
A number of the authors are also microbiologists who are interested not only in the presence and absence of microbes, but in their growth rates. A seminal work estimating growth rates was previously published by the Segal lab [], yet their work is not easily available to clinicians in widely used metagenomics pipelines. This method uses the pattern of mapped read distributions of metagenomic reads to bacterial genomes. The peak to trough ratio of reads is then calculated.
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