System requirements

CLC Microbial Genomics Module 24.0.1 is for use with CLC Genomics Workbench version 24.0.1 or newer. The system requirements for CLC Genomics Workbench are provided at

The system requirements for CLC Microbial Genomics Module are the same as those for CLC Genomics Workbench, except for the following:

Special requirements for the MLST Scheme tools

The system requirement for the MLST Scheme tools depends on the size of the MLST schemes (both the number of alleles and the number of sequence types). A laptop with 16GB of memory is normally sufficient for 7-gene schemes or cgMLST schemes based on a moderate number of isolates. Downloading and constructing or typing with larger schemes may require more memory, and in general we recommend at least 64GB of memory when working with cg/wgMLST schemes based on more than 100 isolates.

Special requirements for OTU Clustering

The memory requirement of Reference based OTU clustering depends on the size of the reference database used; more and longer sequences require more run time and memory. Newer version of common choices (e.g. the full SILVA SSU database) are likely to be too large for a 16 GB machine. Instead we recommend using clustered databases (e.g. the SILVA SSU 99% database) and/or otherwise filtering and subsetting the database, to minimize its size.

Special requirements for Classify Long Read Amplicons

The memory requirement for Classify Long Read Amplicons depends on both sample size and the size of reference database. The following are examples of maximum memory usage given different 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 like the unclustered SILVA SSU database, are expected to require more than 32GB of available memory.

Special requirements for Taxonomic Profiling

The performance of the Taxonomic Profiling tool depends on the reference database used - the more complete a database, the better the taxonomic profiling. However, running Taxonomic Profiling with a given database size will require at least the same amount of memory. For example, a 14 GB database requires at least 16 GB of RAM, and a 56 GB database requires a minimum of 64 GB RAM. When creating your reference database with the Download Custom Microbial Reference Database tool, you will get a warning about the memory requirements needed for running the Taxonomic Profiling tool with this database.

Special requirements for De Novo Assemble Metagenome

At least 16 GB RAM is recommended for running De Novo Assemble Metagenome.