System requirements

In addition to meeting the system requirements of the CLC Genomics Workbench or the CLC Genomics Server, the following requirements must be met:

Special requirements for MLST typing

The system requirements for MLST typing depend on both the number of alleles and the number of sequence types in the MLST scheme. For 7-gene schemes or cgMLST schemes based on a moderate number of isolates, a laptop with 16 GB of RAM is generally sufficient. However, downloading, constructing, or typing with larger schemes may require additional memory. We recommend at least 64 GB of RAM when working with cgMLST or wgMLST schemes derived from more than 100 isolates.

Special requirements for OTU Clustering

The system requirements for performing reference based OTU Clustering depend on the size of the reference database. Newer releases of commonly used databases (e.g., the SILVA SSU database) are likely to be too large for a laptop with 16 GB of RAM. We recommend using clustered databases (such as the SILVA SSU 99% database) and/or filtering the reference database to reduce its size.

Special requirements for Classify Long Read Amplicons

The system requirements for Classify Long Read Amplicons depend on both the sample size and the size of the reference database. The table below provides examples of memory usage for different combinations of sample and database sizes.

Sample size Database size Memory usage
100,000 reads 9 MB / 50,000 sequences 15 GB
100,000 reads 13 MB / 27,000 sequences 10 GB
1,000,000 reads 9 MB / 50,000 sequences 25 GB
1,000,000 reads 13 MB / 27,000 sequences MB 20 GB

Large reference databases (e.g., the SILVA SSU database) require more than 32 GB of RAM.

Special requirements for Taxonomic Profiling

The system requirements for Taxonomic Profiling depend on the size of the reference database. In general, more complete databases provide better taxonomic profiling results, but they also require more memory to run. As a guideline, at least as much RAM as the size of the reference database should be available. For example, a 14 GB database requires a minimum of 16 GB of RAM, while a 56 GB database requires at least 64 GB of RAM. Download Custom Microbial Reference Database displays a warning indicating the memory requirements for running Taxonomic Profiling with the generated database.

Special requirements for Create Whole Metagenome Index

The system requirements for Create Whole Metagenome Index depend on the size of the reference database. Approximately 1.7 bytes of temporary space are needed per base in the database. For example, a 90 Gb database requires about 90 Gb x 1.7 GB/Gb $ \approx$ 150 GB of free temporary disk space.

Special requirements for De Novo Assemble Small Genome

On Linux, De Novo Assemble Small Genome additionally requires supported versions of SUSE Linux Enterprise Server 15.3 and later.

Compatibility

CLC Microbial Genomics Module 26.0 and CLC Microbial Genomics Server Extension 26.0 can be installed on CLC Genomics Workbench 26.0 and CLC Genomics Server 26.0, respectively, and on later versions in the same major release line.