Benchmarking tools for de novo microbial assembly

A recent paper Souvorov et al. presented a new SKESA assembler, which is claimed to be highly efficient and accurate for assembling microbial isolates. Their results have motivated us to reconsider the default SPAdes behavior for performing the most “basic” of assemblies — assembling microbial isolates. Competitors often show us our weak points and countless improvements in our pipelines were inspired by the solutions pioneered by the authors of IDBA-UD,