Program wf-mag demo

The co-assembly samples are named based on the metadata that was chosen to perform co-assembly. If the runs are publicly available, specify them in the runs. Singularity 3. Snakemake version 5. It will also download the relevant singularity containers so the relevant software needed for our pipeline can be used. Alternatively, the tools can be manually downloaded from:.

CheckM version 1. Bowtie version 2. Prokka version 1. CMSeq version 1. Next generate a Mash sketch of the database with default k-mer and sketch size from the main directory using:. Change directory to this folder. To run pipeline on the small gut dataset specified in runs. The CPU time for the demo dataset and the cluster configuration file provided is as follows:.

For a walk-through of this pipeline, please visit: Saheb Kashaf, S. Recovering prokaryotic genomes from host-associated, short-read shotgun metagenomic sequencing data. Nat Protoc To generate results from the paper associated with this pipeline, please select a figure to reproduce in the Snakefile. Skip to content. Star Recovery of prokaryotic genomes from shotgun metagenomic sequencing data View license.

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