De Novo Assemble Metagenome
The De Novo Assemble Metagenome tool is designed for de novo assembly of short sequencing reads from mixed-community samples, such as soil, ocean water, or human gut.
For assembly of single-organism isolates, use the De Novo Assemble Small Genome tool (De Novo Assemble Small Genome), or a de novo assembly tool from CLC Genomics Workbench (https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=De_Novo_sequencing.html).
The De Novo Assemble Metagenome tool produces a list of contigs that can be used for downstream analysis.
Before assembly, adapters should be removed from the sequencing reads using the Trim Reads tool (https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Trim_Reads.html). 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 can 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.
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