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aquamis website  

AQUAMIS is a pipeline for routine assembly and quality assessment of microbial isolate sequencing experiments. It is based on Snakemake and includes the following tools:

  • fastp for read trimming and read QC
  • shovill (based on Spades) for de-novo assembly
  • mash for reference search and species determination
  • QUAST v5 (including BUSCO) for assembly QC
  • confindr for inter and intra genus contamination analysis
  • kraken2 for read and assembly based taxonomic profiling

Environment Modules

Run module spider aquamis to find out what environment modules are available for this application.

System Variables

  • HPC_AQUAMIS_DIR - installation directory
  • HPC_AQUAMIS_BIN - executable directory
  • HPC_AQUAMIS_REF - reference database directory


If you publish research that uses aquamis you have to cite it as follows:

Deneke, C.; Brendebach, H.; Uelze, L.; Borowiak, M.; Malorny, B.; Tausch, S.H. Species-Specific Quality Control, Assembly and Contamination Detection in Microbial Isolate Sequences with AQUAMIS Genes 2021, 12, 644. doi:10.3390/genes12050644