The Metagenomics/population assembly workflow offers both reference-guided (“templated”) and de novo assembly options, with and without removal of host DNA. The default parameters for this workflow have been optimized to take into account the short read lengths and presence of repetitive DNA sequences common to metagenomic and 16S rRNA data.
To follow this workflow, select Metagenomics/population assembly in the Choose Assembly Workflow screen, and any option in the Choose Assembly Type screen. SeqMan NGen automatically pre-filters Metagenomics/16S data prior to assembly by removing redundant, low-quality sequences.
•If you select one of the two options involving host removal, the workflow will include the Input Host Files screen. Many genome packages are available for free download from the DNASTAR website. SeqMan NGen will remove host DNA first, then assemble the remaining data using the method you specified (templated or de novo).
•If you select a templated option, the workflow will include the Input Reference Sequences screen. Reference sequences can be downloaded from any of a number of available 16s rRNA databases,, such as Silva, Greengenes or the Ribosomal Database Project (RDP).
•In the Input Sequence Files and Define Experiments or Individual Replicates screen, you may enter either single-end or paired-end reads. If available, paired-end reads are recommended for highest accuracy.