De Novo Assemble Metagenome

Before assembly, adapters should be removed from sequences. This can be done using Trim Reads ( The presence of adapters can result in the assembler trying to join regions that are not biologically relevant, leading to an assembly taking a long time and yielding misleading results.

Quality trimming before assembly is not generally necessary as the assembler itself should weed out or correct bad quality regions. However, trimming of low quality regions may decrease the amount of memory needed for the de novo assembly, which can be an advantage when working with large datasets.

To run the De Novo Assemble Metagenome tool:

        Toolbox | Microbial Genomics Module (Image mgm_folder_closed_flat_16_h_p) | Metagenomics (Image wma_folder_open_flat_16_n_p) | De Novo Assemble Metagenome (Image de_novo_metagenome_16_n_p)

Select the sequence lists or single sequences to assemble.

Set assembly parameters (figure 4.1).

Image DeNovoAssembleMetagenomeParameters
Figure 4.1: Setting parameters for the assembly.

Select Create report to create a summary report containing statistics on input reads and output contigs.

The De Novo Assemble Metagenome output

The De Novo Assemble Metagenome tool will output a list of contigs. If Perform scaffolding was selected, scaffolds will appear at the bottom of the contig list as scaffold_1, scaffold_2, etc.