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crossmapper website  

Crossmapper is an automated bioinformatics pipeline for asessing the rate of read crossmapping when two or more organisms are sequenced as one sample. The software can be used for planning such kind of experimental setups as dual- or multiple RNA-seq (mainly for host-pathogen, symbiont and cohabitant interaction studies), metagenomics studies, sequencing and analysis of hybrid species, allele-specific expression studies, and can be extended for the use in large sequencing facilities for resource optimization.

Environment Modules

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

System Variables

  • HPC_CROSSMAPPER_DIR - installation directory
  • HPC_CROSSMAPPER_BIN - executable directory


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

CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies