Comparison of Velvet to SPAdes assemblies of 14 isolates associated with crown gall
Validation of the Phytopath-type tool
The 16S rDNA sequence from isolate originally labeled as Agrobacterium isolate 14-2641 was analyzed using the Phytopath-type tool. The isolate is labeled in red, as “query_isolate”; inset shows the clade that circumscribes the isolate.
The SPAdes assembler produces high quality assemblies
Genome sequences assembled using Velvet v. 1.2.10 (blue) and SPAdes v. 3.7.0 (orange) were compared based on scaffold N50 and number of scaffolds greater than 1kb in size.
Whole genome alignment of 13-626 assemblies to a close reference sequence indicates collinearity of genomes
The A. radiobacter K84 genome sequence (top) and assemblies of 13-626 generated using SPAdes v. 3.7.0 (middle; 47 scaffolds) and Velvet (bottom; 527 scaffolds) were aligned using Mauve. Shared locally collinear blocks (LCBs) between the reference and the two assemblies are color-coded and connected by color-coded lines. Scaffold and replicon ends are depicted as vertical red lines.