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.

Based on in-silico read simulation and back-mapping to the original genomes of sequenced organisms, Crossmapper allows the users to assess the rate of incorrect unique and multimapped reads to non-corresponding genomes and thus helps to optimize the sequencing parameters such as the read lenght, paired/single-end, mapping parameters, etc., prior of performing the actual sequencing experiment.

To Install please run :

conda install -c gabaldonlab -c bioconda crossmapper