Assemble
The next step in the workflow is to perform de novo assembly with MEGAHIT on the cleaned reads. Captus makes it easy to process many samples in a consistent manner, automatically, and providing a comprehensive Assembly Control HTML report.
MEGAHIT is an extremely fast and robust de novo assembler that is very memory-efficient thanks to the use of a new data structure called succint De Bruijn Graph (sDBG). Most importantly, accuracy is not sacrificed because it was originally designed for assembling metagenomes. Since then, it has been shown to be an excellent generalist assembler as well.
Captus allows you the flexibility to also provide pre-assembled samples. However, we recommend that, whenever you have read data, to assemble it using Captus. For transcriptome assemblies for example, other assemblers will produce lots of redundant contigs (due to isoforms, alleles, etc.) which MEGAHIT tends to collapse into a single contig. This is ideal for phylogenomics (and perhaps also to build non-redundant reference transcriptomes).
If you are analyzing data with extremely high sequencing depth, or you are trying out parameters and want a quick result, Captus can subsample a fixed number of reads prior to assembly.
In case you assembled your reads elsewhere or you want to use only pre-assembled genomes (e.g., downloaded from GenBank), you can jump ahead to the extract command page.
Created by Edgardo M. Ortiz (06.08.2021)
Last modified by Edgardo M. Ortiz (30.05.2022)