CITATION

*********
Citations
*********

Software Citation
=================

If you use the Toboggan software, you must cite:

K. Kloster, P. Kuinke, M.P. O'Brien, F. Reidl, F. Sanchez Villaamil,
B.D. Sullivan, and A. van der Poel. (2017)
Toboggan: Version 1.0. Zenodo. 10.5281/zenodo.821634

..code-block::tex

                  @misc{Toboggan_v1.0,
                    author       = {Kyle Kloster and
                                    Philipp Kuinke and
                                    Michael P. O'Brien and
                                    Felix Reidl and
                                    Fernando Sanchez Villaamil and
                                    Blair D. Sullivan and
                                    Andrew van der Poel},
                    title        = {Toboggan: Version 1.0},
                    month        = jun,
                    year         = 2017,
                    doi          = {10.5281/zenodo.821634},
                    url          = {http://dx.doi.org/10.5281/zenodo.821634}
                  }

If you use any of our published algorithms or heuristics you should *also*
cite the relevant paper(s) as directed below.

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

The methods in lib:toboggan (which are used in the main pipeline :program:`toboggan.py`) implement the fpt flow decomposition algorithm described in:

    K. Kloster, P. Kuinke, M.P. O'Brien, F. Reidl, F. Sanchez Villaamil, B.D. Sullivan, and A. van der Poel. (2017)
   A practical fpt algorithm for Flow Decomposition and transcript assembly.
   ArXiv:1706.07851. 2017.


.. code-block:: tex

@article{toboggan2017,
  author    = {
               Kyle Kloster and
               Philipp Kuinke and
               Michael P. O'Brien and
               Felix Reidl and
               Fernando Sanchez Villaamil and
               Blair D. Sullivan and
               Andrew van der Poel},
  title     = {A practical fpt algorithm for Flow Decomposition and transcript assembly},
  volume    = {abs/1706.07851},
  year      = {2017},
  url       = {https://arxiv.org/abs/1706.07851},
}