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CCMetagen website  

CCMetagen is a pipeline to classify organisms in metagenomes or metatranscriptomes accurately.

Environment Modules

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

System Variables

  • HPC_CCMETAGEN_DIR - installation directory
  • HPC_CCMETAGEN_BIN - executable directory
  • HPC_CCMETAGEN_REF - database reference directory


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

Marcelino VR, Clausen PT, Buchman J, Wille M, Iredell JR, Meyer W, Lund O, Sorrell T, Holmes EC. 2019. CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data. Genome Biology. 2020 Dec;21(1):1-5.

Clausen PT, Aarestrup FM, Lund O. 2018. Rapid and precise alignment of raw reads against redundant databases with KMA. BMC bioinformatics. 2018 Dec;19(1):307.