Compression-based distance (CBD) is a simple, rapid, and accurate method to efficiently assess differences in microbiota samples. CBD characterizes the similarities between microbial communities via the amount of repetition or overlap in order to determine microbial community distance. CBD relies on the fact that more repetitive data is the more it can be compressed. By combining 16S rRNA hypervariable tag data from different samples and assessing the relative amounts of compression, there is a proxy for the similarities between the communities. The amount of compression is converted to a distance by taking compression gained by combining the datasets over the total compressed size of the individual datasets. The distance has a value with a minimum of 0 meaning the communities are the same and a maximum of 1 meaning the communities are completely different.
The Compression-Based Distance server supports the following configuration variables:
- default_url: The default URL for this server's service endpoint.
- shock_url: URL for the Shock service endpoint. The Shock service is used to transfer input sequence files to the server and return the computed distance matrix file to the client.
- userandjobstate_url: URL of the User and Job State service endpoint. The UJS service is used to manage the jobs that build a distance matrix.
- work_folder_path: Path to work folder containing a sub-folders for each running job. The intermediate files created by the build_matrix() method are stored in this location.
- num_pool_processes: Number of processes in multiprocess pool. A larger value increases the number of tasks running in parallel when building a distance matrix. Default value is 5.