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 Join Contigs

Most types of analyses in the Join Contigs tool run in a single thread. An exception is the long reads scaffolding option that utilize the CLC read mapper and is therefore able to use all available cores in a system. As mapping reads to contigs is one of the most time consuming steps when performing long reads scaffolding it is often an advantage to use a machine with many cores for this type of analysis.

The memory required for joining contigs depends on several factors as described below and it is not possible to predict the maximum memory consumption for an analysis. For most bacterial data sets it will be possible to run the Join Contigs tool on a machine that fulfills the system requirements of the CLC platform software. Some examples where more memory can be needed:

To help estimate the required memory consumption both for bacterial sized genomes and larger genomes some examples are given below. The memory consumption was measured on a machine with four cores, and the memory consumption for the long reads scaffolding can be larger for machines with more cores.

Organism Analysis Reads Memory required
E. coli Long read scaffolding + 273,232 454 reads 5GB
(4.6 Mbp) Reference based scaffolding avg. length=514bp  
S. cerevisiae Paired read scaffolding 22,262,792 5GB
(12.5 Mbp)   Illumina reads  
E. coli Long read scaffolding 163,478 PacBio reads 8GB
(4.6 Mbp)   avg. length=6.5Kbp  
B. lactucae Long read scaffolding 6,086,612 PacBio reads 10GB
(88 Mbp)   avg. length 2.4Kbp  

Compatibility

CLC Genome Finishing Module 26.0 and CLC Genome Finishing 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.