Consensus generation in these samples is similar to haploid genome assembly, and existing assemblers are expected to work reasonably well since variants can be treated as sequencing errors and removed from the data.
However, as over 90% of microbes in metagenomic data are unknown (Wooley et al., 2010), de novo assemblers are needed to assemble reads without any reference genomes.
Currently available genome assemblers are not designed to assemble polyploids and the resulting assemblies are often fragmented [ 18], chimeric [ 19] and/or contain false segmental duplications [ 20].
Up to now, the performances of assembling repeats of these current assemblers are very poor.
This is not entirely unexpected for the MIRA assemblies, as overlap graph based assemblers are less tolerant of high coverage [ 42].
In summary, these results suggest that de novo transcriptome assemblers are more appropriate for assembling small mt genomes present in variable copy numbers in total DNA mixed-samples.
Although whole genome assemblers are not designed to assemble metagenomic samples, they are being used for metagenomics due to the lack of assemblers capable of dealing with metagenomic samples.
Furthermore, assemblers are mainly built for assembling all reads into a single sequence, which is exactly the opposite of the separation of sequences of different organisms, which metagenomics strives for.
All four assemblers are claimed to yield longer assemblies and more representative taxonomic representations than conventional assemblers.
Shippers are good at shipping things in general; credit card companies are good at managing credit risks, regardless of where customers buy; electronics assemblers are good at all sorts of assembly.
And while assembly is heavily based in China, electronics assemblers are rapidly adapting their supply chains to mitigate the damage of tariffs by moving factories to Vietnam, India, and elsewhere.
