Genome Polishing Benchmarks: SeqMan NGen vs. Three Open-Source Tools
What is “genome polishing”?
“Genome polishing,” sometimes referred to as “genome finishing,” is a workflow in which assembly software searches for local misassemblies and other inconsistencies in a draft genome assembly and then corrects them. Genome polishing can be used to create hybrid assemblies with Illumina data and long read sequencing data and is especially valuable for enhancing assembly results where there are concerns about single molecule or nanopore sequencing accuracy.
Our benchmarking test
This week, we published a white paper showing accuracy and other statistical benchmarks for SeqMan NGen’s genome polishing workflow versus several open-source tools. The SeqMan NGen workflow is called “Short read polishing of a long-read draft genome” and was released earlier this year as part of Lasergene 17.0.
The first step in the genome polishing workflow was to use Canu to create draft genome assemblies for six eukaryotic and prokaryotic species from long-read sequencing data. These data sets were composed of PacBio reads or Oxford Nanopore Technologies “MinION” sequencing reads.
Illumina reads were then utilized to polish the assembly using one of three tools: SeqMan NGen, Pilon or SPAdes. This created either a PacBio-Illumina hybrid assembly or a MinION-Illumina hybrid assembly, depending on the sequencing technology used in each data set. The assemblies were then evaluated on various metrics for accuracy and genome coverage using This was done using QUAST 5.0.2, a quality assessment tool for evaluating and comparing genome assemblies. The unpolished Canu assemblies were also included in the QUAST analysis.
What did we learn?
What were the strengths and weaknesses of each tool? Which tool was the overall “winner” for genome finishing accuracy and ease of use? Which tool provides the ability to do downstream analysis of the completed hybrid assemblies?
To find out, view the white paper using the link below.
Try it yourself!
Try DNASTAR’s genome polishing workflow yourself with a fully-functional free trial of Lasergene. Use SeqMan NGen to create the hybrid assembly, then use SeqMan Pro and/or SeqMan Ultra to do downstream analysis, as shown in the image below.
Click the button below to get started.