Fig. 2

Overall performance and quality assessment of the SGP hybrid assembly pipeline. a Assembly statistics of 20 genomes subjected to the SGP hybrid assembly pipeline. The bar plot depicts genome size, GC content, N50 value, and assembly completeness of individual genomes (orange circles indicating complete assemblies and blue triangles indicating fragmented assemblies). b Evaluating the performance of SGP hybrid assembly by performing parallel multiplexed Illumina and PacBio sequencing on 9 genomes. The bar plot depicts assembly statistics of Illumina short-read assembly, hybrid assembly of barcoded Illumina and PacBio reads (Barcoded_Hybrid), SGP hybrid assembly, long-read assembly of barcoded PacBio reads polished using long reads (Flye) or short Illumina reads (Flye_Pilon). c Reference-free assembly validation: qualities of assemblies were assessed by mapping high-quality barcoded Illumina reads of each genome to its corresponding assemblies using Breseq. The top panel shows the frequency of single base substitutions, the middle panel shows the frequency of insertion sequences (unresolved repeat elements identified as small contigs with higher read coverages compared to other regions of the chromosome), and the bottom panel shows the frequency of small insertion-deletions (indels) in various assemblies of each genome. d Dot plot showing the ability of different assembly approaches to resolve multiple copies of the 16S ribosomal RNA gene within each genome. Position of each dot on x-axis depicts the total number of 16S rRNA gene copy numbers detected within each assembly. Numbers within dots indicate intragenomic heterogeneity (sequence variants) among 16S rRNA genes of each assembly