update documentation to link preprint

README.md

@@ -20,7 +20,9 @@ This will put the DNAscent executable into the DNAscent/bin directory.  A typica
 Please see the [documentation](https://dnascent.readthedocs.io) for detailed usage instructions, descriptions of DNAscent's subprograms, and an example workflow.
 
 ## Citation
-Muller CA, Boemo MA, Spingardi P, Kessler BM, Kriaucionis S, Simpson JT, Nieduszynski CA. Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads. *Nature Methods* 2019;16:429-436. [[Journal Link](https://www.nature.com/articles/s41592-019-0394-y)]
+Please cite the following if you use DNAscent for your research:
+- Boemo, MA. DNAscent v2: Detecting Replication Forks in Nanopore Sequencing Data with Deep Learning. *bioRxiv* 2020. [[Preprint Link](https://doi.org/10.1101/2020.11.04.368225)]
+- Muller CA, Boemo MA, Spingardi P, Kessler BM, Kriaucionis S, Simpson JT, Nieduszynski CA. Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads. *Nature Methods* 2019;16:429-436. [[Journal Link](https://www.nature.com/articles/s41592-019-0394-y)]
 
 ## Questions and Bugs
 Should any bugs arise or if you have basic usage questions, please raise a [GitHub issue](https://github.com/MBoemo/DNAscent/issues). For more detailed discussions or collaborations, please Email Michael Boemo at [email protected].

docs/source/index.rst

@@ -34,6 +34,8 @@ Publications
 
 Please cite the following publication if you use DNAscent for your research: 
 
+Boemo, MA. DNAscent v2: Detecting Replication Forks in Nanopore Sequencing Data with Deep Learning. bioRxiv 2020. [`Preprint DOI <https://doi.org/10.1101/2020.11.04.368225>`_]
+
 Muller CA, Boemo MA, Spingardi P, Kessler, BM, Kriaucionis S, Simpson JT, Nieduszynski CA. Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads. Nature Methods 2019;16:429-436. [`Journal DOI <https://doi.org/10.1038/s41592-019-0394-y>`_]
 
 Bugs, Questions, and Comments

docs/source/releaseNotes.rst

@@ -11,9 +11,9 @@ v2.0.2
 * Support for BrdU detection on GPUs,
 * ``DNAscent forkSense`` to call replication origins and termination sites in both synchronously and asynchronously replicating cells at any point in S-phase,
 * ``DNAscent align`` to align nanopore signals to reference,
-* Significant increases to replication origin calling accuracy,
+* Significant increases to replication origin calling accuracy and sensitivity,
 * Visualisation utility for plotting output of multiple DNAscent executables as bedgraphs,
-* Released with `Boemo, M.A. DNAscent v2: Detecting Replication Forks in Nanopore Sequencing Data with Deep Learning. bioRxiv 2020.
+* Released with `Boemo, MA. DNAscent v2: Detecting Replication Forks in Nanopore Sequencing Data with Deep Learning. bioRxiv 2020. <https://doi.org/10.1101/2020.11.04.368225>`_.
 
 v1.0.0
 -----------------
@@ -22,7 +22,7 @@ v1.0.0
 * Improvements to BrdU detection accuracy,
 * ``DNAscent train`` to train Guassian mixture models from nanopolish eventalign.
 
-v0.1
+v0.1.0
 -----------------
 
 * HMM-based BrdU detection at ~160 thymidine-containing 6mers,