The de novo assembly of the datasets resulted in 187.168 contigs for the combined dataset integrating 82% of the reads, 129.402 contigs for the enzyme AciI (reads: 70%), and 111.390 contigs for HpaII (reads: 87%).
For comparing the assembly performance, we created another dataset with the same number of reads from a single strain, E.Coli strain 536 (represents the isolate assembly), and assembled it using the different k-mer size values used for assembly of the strains dataset.
The first approach gave results more consistent with the Unigene and TIGR Wheat Gene Index assembly data with respect to contig number, suggesting that PHRAP was less appropriate for assembly of the large dataset used in this study.
Although most of the full-length ORFs in Table 1 were taken directly from the metagenome, several were manually reconstructed from fragmented genes identified in the assembly of the metagenomic dataset.
The de novo assembly of the whole dataset was time-consuming due to memory issues, so we used Diginorm (Digital normalization with khmer, [ 80]) to normalize the raw data digitally.
In the assembly of the UCRNP2 dataset (see Table-S2; Additional file 1), ABySS and IDBA-UD show higher g1 quality performance as compared to the current draft genome at both contigs and scaffolds levels (see Fig. S2; Additional file 2).
The degree of similarity between O. marina datasets was further explored based on a CAP3 [ 31] assembly of the combined datasets (see following section).
Though knowledge of LSV derives from PRICE assemblies of this dataset, the reference LSV1 and LSV2 genome sequences (HQ871931 and HQ888865, respectively) derive from Sanger sequencing of reverse transcription PCR products amplified from a separate sample (Runckel et al. 2011).
As for the runtimes, the assembly of the whole grouper dataset used ~50 days with ~600 GB peak RAM usage on a virtual machine of 32 cores and 1 TB RAM, and the assembly of the PE subset used 7.2 days with ~390 GB peak RAM usage on a physical machine of 40 cores and 1.5TB RAM.
At the scaffolds level, Velvet produces the best g1 quality metrics for the assemblies of the PST21 dataset.
