The assemblers used for the de novo and hybrid assembly, their respective versions and assembly recipes are provided in the Supplementary Information (Section S1).
The assemblers selected are based on two different mathematical models for assembly: 'Greedy' and 'Overlap-Layout-Consensus' (OLC).
The assemblers also differed in the average length of contigs produced.
The assemblers were nevertheless generally able to recover at least a single genome from a highly similar group of genomes.
The read length was 100 bp, error rate was 1% and the insert distance followed a normal distribution with mean 250 bp and standard deviation 25 bp. Figure 4 shows the quality of the assembly results of the assemblers for different levels of completeness.
Because of their minute size, the only practical way to fabricate large or large quantities of entities is for the assemblers to first assemble copies of themselves, which then all work in parallel.
The assembly should be carefully evaluated because most of the assemblers were developed for genome assembly and are not designed to deal with the heterogeneity of metagenomic datasets.
In our study, we evaluate the assemblers based on their assembly performance parameters, which are divided into computational as well as quality parameters.
All the assemblers encounter various difficulties in assembling the Wolbachia sp. dataset into long contigs, which is probably due to a higher error rate in the reads.
The ideal assemblers achieve an ideal trade-off between running time, memory consumption, and quality of assemblies (i.e., the assemblers that belong to the fastest class, most memory-efficient class, and high-quality class).
Although we were testing different genome assemblers and assembly parameters, we examined the assemblies of the most highly amplified nanochromosome and the longest nanochromosome, because they present challenging cases for the assemblers and were often not completely assembled.
