xenomapper - mapping mixed reads from two species
Xenomapper is a utility for post processing mapped reads that have been aligned to a primary genome and a secondary genome and binning reads into species specific, multimapping in each species, unmapped and unassigned bins. It can be used on single end or paired end sequencing data. In paired end data evidence of sequence specificity for either read will be used to assign both reads.
Use cases include xenografts of human cancers and host pathogen interactions.
Xenomapper is most effective with mapped reads that include an XS or ZS score that gives the mapping score of the next best read. These include Bowtie2 (Langmead, 2012) and HISAT (Kim, 2015).
Xenomapper requires python 3.3 or higher and is tested on linux and MacOS with CPython and pypy3. For bam file decoding samtools must be installed.
Installing from the Python Package Index with pip is the easiest option:
pip3 install xenomapper
Alternatively if you would like to install from the github repository
git clone https://github.com/genomematt/xenomapper pip3 install --upgrade xenomapper
Although the repository tests by continuous integration with TravisCI its good practice to run the tests locally and check your install works correctly. The tests are run with the following command:
python3 -m xenomapper.tests.test_all
All users should upgrade to v0.5.0 or higher as earlier versions have known bugs.
Xenomapper is published in the Journal of Open Source Software. Please cite the paper in academic publications DOI:10.21105.joss.00018.