Assembly

Assembling a metagenome or metatranscriptome

Since MGX 2.0, we support the assembly and analysis of both metagenomes and metatranscriptomes; for this, we provide workflows targeting QC, (co-)assembly, gene prediction, taxonomic binning, completeness assessment, and abundance quantification.

For metatranscriptomes, an additional step is implemented for the removal of ribosomal RNA sequences prior to the assembly, and binning is not performed.

To create an assembly, select all sequencing runs that should be co-assembled within the Project Explorer window and select the Assemble entry from the context menu. Single-end data can be included into this process, but the corresponding workflows require that at least one paired-end dataset is provided, as this yields better assembly results.

Also, only paired-end data is used for the taxonomic binning step, and we recommend to co-assemble multiple paired-end datasets for an improved binning outcome.

The assembly wizard requires to specify a name for the new assembly, and once the assembly workflow has been submitted, its state can be monitored from the Job Monitor.