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,
We are happy to announce that we have just released new SPAdes 3.7.0. This version includes metaSPAdes metagenomic pipeline and many other improvements and fixes.
Please note that SPAdes is not intended for large genomes (e.g. mammalian size genomes). Should you decide to use SPAdes for a larger genome, please be aware that you are doing it at your own risk.
rnaQUAST is a tool for evaluating quality of transcriptome assemblies using reference genome and gene database. You can download here the first stable release.