XenoMapper 1.0.0

Xenomapper

Xenomapper is a utility for post processing Bowtie2 (Langmead, 2012) 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 in mouse and host pathogen interactions.

Installation

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 python3 -m xenomapper.tests.test_all

All users should upgrade to v0.5.0 or higher

Citing Xenomapper

Currently Xenomapper is unpublished, but this repository does have a DOI identifier for each release you can use to cite the code.