aquamis¶

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.

Environment Variables¶

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

Categories¶

biology, genomics