Merge pull request #64 from jbloomlab/citation_info

Citation info

README.rst

@@ -14,12 +14,17 @@ alignparse
 .. image:: https://zenodo.org/badge/194140958.svg
    :target: https://zenodo.org/badge/latestdoi/194140958
 
+.. image:: https://joss.theoj.org/papers/10.21105/joss.01915/status.svg
+   :target: https://doi.org/10.21105/joss.01915
+
 ``alignparse`` is a Python package written by `the Bloom lab <https://research.fhcrc.org/bloom/en.html>`_. 
 It is designed to align long sequencing reads (such as those from PacBio circular consensus sequencing) to targets, filter these alignments based on user-provided specifications, and parse out user-defined sequence features.
 For each read that passes the filters, information about the features (e.g. accuracy, sequence, mutations) is retained for further analyses. 
 
 See the `alignparse documentation <https://jbloomlab.github.io/alignparse>`_ for details on how to install and use ``alignparse``.
 
+Please `cite alignparse <https://jbloomlab.github.io/alignparse/acknowledgements.html>`_ if you use it in your work.
+
 The source code is `on GitHub <https://github.com/jbloomlab/alignparse>`_.
 
 To contribute to this package, read the instructions in `CONTRIBUTING.rst <CONTRIBUTING.rst>`_.

docs/acknowledgments.rst

@@ -1,5 +1,12 @@
 Acknowledgements
 -----------------
-``alignparse`` is written by `the Bloom lab <https://research.fhcrc.org/bloom/en.html>`_.
 
-See https://github.com/jbloomlab/alignparse/graphs/contributors for the full list of contributors.
+`alignparse <https://jbloomlab.github.io/alignparse/>`_ is written by `the Bloom lab <https://research.fhcrc.org/bloom/en.html>`_.
+
+For the full list of contributors to `alignparse <https://jbloomlab.github.io/alignparse/>`_, `see here <https://github.com/jbloomlab/alignparse/graphs/contributors>`_.
+
+If you use `alignparse <https://jbloomlab.github.io/alignparse/>`_ in your research, please cite the following reference:
+
+Crawford KHD and Bloom JD. `"alignparse: A Python package for parsing complex features from high-throughput long-read sequencing." <https://doi.org/10.21105/joss.01915>`_. *Journal of Open Source Software*, 4:44, 1915 (2019).
+
+If you use the :mod:`alignparse.minimap2` module to run `minimap2 <https://github.com/lh3/minimap2>`_, please also cite the `reference for minimap2 <https://academic.oup.com/bioinformatics/article/34/18/3094/4994778>`_.

docs/examples.rst

@@ -2,11 +2,11 @@
 Examples
 =========
 
-The ``alignparse`` package is designed to aid in the analysis of long-read sequencing of user-defined amplicons. Major functionaly includes:
+The `alignparse <https://jbloomlab.github.io/alignparse/>`_ package is designed to aid in the analysis of long-read sequencing of user-defined amplicons. Major functionaly includes:
     - The :class:`alignparse.targets.Targets` class for defining reference sequence `Targets`, aligning reads, and parsing features from aligned reads.
     - The :mod:`alignparse.consensus` for analyzing mutations and sequencing accuracy, especially for sequences grouped by shared barcodes.
 
-Here are some examples that demonstrate how to utilize this functionality and other aspects of the ``alignparse`` package:
+Here are some examples that demonstrate how to utilize this functionality and other aspects of the `alignparse <https://jbloomlab.github.io/alignparse/>`_ package:
 
 .. toctree::
    :maxdepth: 1

docs/index.rst

@@ -1,11 +1,15 @@
 ``alignparse`` documentation
 ===================================================
 
-``alignparse`` is a Python package written by `the Bloom lab <https://research.fhcrc.org/bloom/en.html>`_.
+`alignparse <https://jbloomlab.github.io/alignparse/>`_ is a Python package written by `the Bloom lab <https://research.fhcrc.org/bloom/en.html>`_.
 It is designed to align long sequencing reads (such as those from PacBio circular consensus sequencing) to `targets`, filter these alignments based on user-provided specifications, and parse out user-defined sequence `features`. 
 
 For each read that passes the user-defined filters, the user can define what information about each feature (e.g. sequence, mutations, and sequencing accuracy) should be retained for further analyses. The `alignparse.consensus` module provides tools for such further analyses, including analyzing mutations identified in sequence features and defining consensus sequences from barcoded sequencing reads.
 
+The `alignparse source code <https://github.com/jbloomlab/alignparse>`_ is freely available on GitHub.
+
+If you use `alignparse <https://jbloomlab.github.io/alignparse/>`_ for your work, please cite the references in `Acknowledgements <https://jbloomlab.github.io/alignparse/acknowledgements.html>`_.
+
 See below for information and examples of how to use this package.
 
 Contents

docs/installation.rst

@@ -1,21 +1,19 @@
 Installation
 --------------
 
-``alignparse`` requires Python 3.6 or higher and is currently tested on Python 3.6 and 3.7. 
+`alignparse <https://jbloomlab.github.io/alignparse/>`_ requires Python 3.6 or higher and is currently tested on Python 3.6 and 3.7. 
 A Mac OS X or Linux operating system is also required.
 
-The easiest way to install ``alignparse`` is from `PyPI <https://pypi.org/>`_ using `pip <https://pip.pypa.io>`_ with::
+The easiest way to install `alignparse <https://jbloomlab.github.io/alignparse/>`_ is from `PyPI <https://pypi.org/>`_ using `pip <https://pip.pypa.io>`_ with::
 
     pip install alignparse
 
-Note that installing the dependency ``pysam`` may require additional packages on the host system.
+Note that installing the dependency `pysam <https://pysam.readthedocs.io/en/latest/api.html>`_ may require additional packages on the host system.
 See the `pysam documentation <https://pysam.readthedocs.io/en/latest/installation.html#pypi-installation>`_ for more details.
 
-The source code for ``alignparse`` is available on GitHub at https://github.com/jbloomlab/alignparse.
-
 In order to use the :mod:`alignparse.minimap2` module, you need to install the `minimap2 <https://github.com/lh3/minimap2>`_ executable (version 2.17 or higher).
 You can do that via the `bioconda recipe <https://bioconda.github.io/recipes/minimap2/README.html>`_ or from the program's release page `as described here <https://github.com/lh3/minimap2#install>`_.
 
-An ``environment.yml`` file is provided with the source code. This can be used to create a `conda environment <https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html>`_ that installs ``alignparse`` and its dependencies using::
+An ``environment.yml`` file is provided with the source code. This can be used to create a `conda environment <https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html>`_ that installs `alignparse <https://jbloomlab.github.io/alignparse/>`_ and its dependencies using::
 
     conda env create -f environment.yml

docs/package_index.rst

@@ -1,4 +1,4 @@
-package index
+Package index
 =============
 
 * :ref:`genindex`