xenomapper - mapping mixed reads from two species
Project description
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Currently Xenomapper is unpublished, but this repository does have a DOI identifier for each release you can use to cite the code.
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