Difference between revisions of "Aquamis"
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| + | * HPC_{{uc:{{#var:app}}}}_REF - reference database directory | ||
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Latest revision as of 22:07, 20 October 2023
Description
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
Citation
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