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Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem

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disambiguate

============

Disambiguation algorithm for reads aligned to two species (e.g. human and mouse genomes) from
Tophat, Hisat2, STAR or BWA mem. Both a Python and C++ implementation are offered. The Python
implementation has a dependency on the Pysam module. The C++ implementation depends on the
availability of zlib and the Bamtools C++ API. For STAR alignments it is highly recommended
to include the NM tag in the output when performing alignment (in fact this is a requirement
for the C++ version).

Differences between the Python and C++ versions:
1. The Python version can do natural name sorting of the reads (a necessary step) internally
but for the C++ version the input BAM files _must_ be natural name sorted (internal natural name sorting not
supported).
2. The flag -s (samplename prefix) must be provided as an input parameter to the C++ binary

For usage help, run disambiguate.py as-is.

To compile the C++ program, use the following syntax in the same folder where the code is:
```
c++ -I /path/to/bamtools_c_api/include/ -I./ -L /path/to/bamtools_c_api/lib/ -o disambiguate dismain.cpp -lz -lbamtools
```

Note, the disambiguate C++ source _must_ be compiled against bamtools version [2.4.0](https://github.com/pezmaster31/bamtools/releases).  The current bamtools release is not supported.

A pre-compiled binary is also available in bioconda http://bioconda.github.io/recipes/ngs-disambiguate/README.html

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.166017.svg)](https://doi.org/10.5281/zenodo.166017)

Citing
------
Ahdesmäki MJ, Gray SR, Johnson JH and Lai Z. Disambiguate: An open-source application for disambiguating two species in next generation sequencing data from grafted samples. F1000Research 2016, 5:2741,
[DOI:10.12688/f1000research.10082.1](https://doi.org/10.12688/f1000research.10082.1)

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