Merge pull request #78 from dib-lab/docs/flesh-out

Flesh out docs

README.rst

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+|kevlar build status| |Test coverage| |MIT licensed|
+
+kevlar
+======
+
+.. figure:: docs/_static/morpheus-kevlar.jpg
+   :alt: What if I told you we don't need alignments to find variants?
+
+Welcome to **kevlar**, software for variant discovery independent of a reference genome!
+
+Where can I find kevlar online?
+-------------------------------
+
+The online home for kevlar is https://github.com/dib-lab/kevlar.
+This includes a source code repository, stable version releases, an issue tracker, and various developer tools.
+Documentation for kevlar can be found at https://kevlar.readthedocs.io.
+
+If you have questions or need help with kevlar, the `GitHub issue tracker <https://github.com/dib-lab/kevlar>`__ should be your first point of contact.
+
+How do I use kevlar?
+--------------------
+
+See kevlar's `installation instructions <http://kevlar.readthedocs.io/en/latest/install.html>`__ and `quick start guide <http://kevlar.readthedocs.io/en/latest/quick-start.html>`__ to learn how to use kevlar.
+
+**Note**: Although a reference genome is not required, it can be utilized to reduce data volume at an early stage in the workflow and reduce the computational demands of subsequent steps.
+
+**Another note**: kevlar development is currently focused almost entirely on finding novel variants in family-based trio and quad experimental designs.
+However, the method lends itself easily to more general experimental designs, which will get more attention and support in the near future.
+
+Contributing
+------------
+
+We welcome contributions to kevlar from the community!
+If you're interested in modifying kevlar or contributing to its ongoing development feel free to send us a message or submit a pull request!.
+
+The kevlar software is a project of the `Lab for Data Intensive Biology <http://ivory.idyll.org/lab/>`__ at UC Davis.
+
+.. |kevlar build status| image:: https://img.shields.io/travis/dib-lab/kevlar.svg
+   :target: https://travis-ci.org/dib-lab/kevlar
+.. |Test coverage| image:: https://img.shields.io/codecov/c/github/dib-lab/kevlar.svg
+   :target: https://codecov.io/github/dib-lab/kevlar
+.. |MIT licensed| image:: https://img.shields.io/badge/license-MIT-blue.svg
+   :target: https://github.com/dib-lab/kevlar/blob/master/LICENSE

docs/index.rst

@@ -16,6 +16,7 @@ That said, the core features of the software are reasonbly well tested, and leve
 
    conduct
    install
+   quick-start
    cli
 
 

docs/quick-start.rst

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+Quick start
+===========
+
+If you have not already done so, install **kevlar** using :doc:`the following instructions <install>`.
+
+A complete listing of all available configuration options for each script can be shown by executing ``kevlar <subcommand> -h`` in the terminal.
+
+----------
+
+#. Compute k-mer abundances
+
+   .. code:: bash
+
+       kevlar count \
+           --case kevlar/tests/data/trio1/case1.fq \
+           --controls kevlar/tests/data/trio1/ctrl[1,2].fq \
+           --ksize 21 \
+           --ctrl_max 0
+
+#. Find "interesting" (potentially novel) k-mers
+
+   .. code:: bash
+
+       kevlar novel \
+           --cases kevlar/tests/data/trio1/case1.counttable \
+           --case_min 8 \
+           --controls kevlar/tests/data/trio1/ctrl[1,2].counttable \
+           --ctrl_max 0 \
+           --ksize 21 \
+           --out case1.novel.unfiltered.augfastq.gz
+           kevlar/tests/data/trio1/case1.fq
+
+#. Recompute k-mer abundances to discard false positives, partition reads by shared novel k-mers
+
+   .. code:: bash
+
+       kevlar filter \
+           --refr kevlar/tests/data/bogus-genome/refr.fa \
+           --contam kevlar/tests/data/bogus-genome/contam1.fa \
+           --min-abund 8 \
+           --ksize 21 \
+           --aug-out case1.novel.filtered.augfastq.gz \
+           --out case1.novel.filtered.fq.gz \
+           --cc-prefix case1 \
+           case1.novel.unfiltered.augfastq.gz
+
+   Currently partitioning is done by ``kevlar filter``, but this will soon be handled by a dedicated ``kevlar partition`` command.
+
+#. Assemble partitioned reads
+
+   .. code:: bash
+
+       kevlar assemble --out case1.cc0.augfasta case1.cc0.augfastq.gz