[MRG] update JOSS paper for v4

.github/workflows/draft-pdf.yml

@@ -0,0 +1,23 @@
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper.pdf

paper.bib

@@ -1,4 +1,4 @@
-@article{ondov2015fast,
+@article{Ondov:2015,
   title={Fast genome and metagenome distance estimation using MinHash},
   author={Ondov, Brian D and Treangen, Todd J and Mallonee, Adam B and Bergman, Nicholas H and Koren, Sergey and Phillippy, Adam M},
   journal={bioRxiv},
@@ -8,3 +8,62 @@ @article{ondov2015fast
   doi={10.1101/029827},
   url={https://doi.org/10.1101/029827}
 }
+
+@article{Brown:2016,
+  doi = {10.21105/joss.00027},
+  url = {https://doi.org/10.21105/joss.00027},
+  year = {2016},
+  publisher = {The Open Journal},
+  volume = {1},
+  number = {5},
+  pages = {27},
+  author = {C. Titus Brown and Luiz Irber},
+  title = {sourmash: a library for MinHash sketching of DNA},
+  journal = {Journal of Open Source Software}
+}
+
+@article{Pierce:2019,
+  doi = {10.12688/f1000research.19675.1},
+  url = {https://doi.org/10.12688/f1000research.19675.1},
+  year = {2019},
+  month = jul,
+  publisher = {F1000 Research Ltd},
+  volume = {8},
+  pages = {1006},
+  author = {N. Tessa Pierce and Luiz Irber and Taylor Reiter and Phillip Brooks and C. Titus Brown},
+  title = {Large-scale sequence comparisons with sourmash},
+  journal = {F1000Research}
+}
+@article{gather,
+  title={Lightweight compositional analysis of metagenomes with FracMinHash and minimum metagenome covers},
+  author={Irber, Luiz Carlos and Brooks, Phillip T and Reiter, Taylor E and Pierce-Ward, N Tessa and Hera, Mahmudur Rahman and Koslicki, David and Brown, C Titus},
+  journal={bioRxiv},
+  year={2022},
+  publisher={Cold Spring Harbor Laboratory}
+}
+
+@article{branchwater,
+  title={Sourmash Branchwater Enables Lightweight Petabyte-Scale Sequence Search},
+  author={Irber, Luiz Carlos and Pierce-Ward, N Tessa and Brown, C Titus},
+  journal={bioRxiv},
+  year={2022},
+  publisher={Cold Spring Harbor Laboratory}
+}
+
+@article{koslicki2019improving,
+  title={Improving minhash via the containment index with applications to metagenomic analysis},
+  author={Koslicki, David and Zabeti, Hooman},
+  journal={Applied Mathematics and Computation},
+  volume={354},
+  pages={206--215},
+  year={2019},
+  publisher={Elsevier}
+}
+
+@article{hera2022debiasing,
+  title={Debiasing FracMinHash and deriving confidence intervals for mutation rates across a wide range of evolutionary distances},
+  author={Hera, Mahmudur Rahman and Pierce-Ward, N Tessa and Koslicki, David},
+  journal={bioRxiv},
+  year={2022},
+  publisher={Cold Spring Harbor Laboratory}
+}

paper.md

@@ -1,32 +1,155 @@
 ---
-title: 'sourmash: a library for MinHash sketching of DNA'
+title: 'sourmash: a tool to quickly search, compare, and analyze genomic and metagenomic data sets'
 tags:
+  - FracMinHash
   - MinHash
   - k-mers
   - Python
+  - Rust
 authors:
- - name: C. Titus Brown
-   orcid: 0000-0001-6001-2677
-   affiliation: University of California, Davis
  - name: Luiz Irber
    orcid: 0000-0003-4371-9659
-   affiliation: University of California, Davis
-date: 13 Sep 2016
+   equal-contrib: true
+   affiliation: 1
+ - name: N. Tessa Pierce-Ward
+   orcid: 0000-0002-2942-5331
+   equal-contrib: true
+   affiliation: 1
+ - name: Mohamed Abuelanin
+   orcid: 0000-0002-3419-4785
+   affiliation: 1
+ - name: Harriet Alexander
+   orcid: 0000-0003-1308-8008
+   affiliation: 2
+ - name: Abhishek Anant
+   orcid:  0000-0002-5751-2010
+   affiliation: 9
+ - name: Keya Barve
+   orcid: 0000-0003-3241-2117
+   affiliation: 1
+ - name: Colton Baumler
+   orcid: 0000-0002-5926-7792
+   affiliation: 1
+ - name: Olga Botvinnik
+   orcid: 0000-0003-4412-7970
+   affiliation: 3
+ - name: Phillip Brooks
+   orcid: 0000-0003-3987-244X
+   affiliation: 1
+ - name: Daniel Dsouza
+   orcid: 0000-0001-7843-8596
+   affiliation: 9
+ - name: Laurent Gautier
+   orcid: 0000-0003-0638-3391
+   affiliation: 9
+ - name: Mahmudur Rahman Hera
+   orcid: 0000-0002-5992-9012
+   affiliation: 4
+ - name: Hannah Eve Houts
+   orcid: 0000-0002-7954-4793
+   affiliation: 1
+ - name: Lisa K. Johnson
+   orcid: 0000-0002-3600-7218
+   affiliation: 1
+ - name: Fabian Klötzl
+   orcid: 0000-0002-6930-0592
+   affiliation: 5
+ - name: David Koslicki
+   orcid: 0000-0002-0640-954X
+   affiliation: 4
+ - name: Marisa Lim
+   orcid: 0000-0003-2097-8818
+   affiliation: 1
+ - name: Ricky Lim
+   orcid: 0000-0003-1313-7076
+   affiliation: 9
+ - name: Ivan Ogasawara
+   orcid: 0000-0001-5049-4289
+   affiliation: 9
+ - name: Taylor Reiter
+   orcid: 0000-0002-7388-421X
+   affiliation: 1
+ - name: Camille Scott
+   orcid: 0000-0001-8822-8779
+   affiliation: 1
+ - name: Andreas Sjödin
+   orcid: 0000-0001-5350-4219
+   affiliation: 6
+ - name: Daniel Standage
+   orcid: 0000-0003-0342-8531
+   affiliation: 7
+ - name: S. Joshua Swamidass
+   orcid: 0000-0003-2191-0778
+   affiliation: 8
+ - name: Connor Tiffany
+   orcid: 0000-0001-8188-7720
+   affiliation: 9
+ - name: Pranathi Vemuri
+   orcid: 0000-0002-5748-9594
+   affiliation: 3
+ - name: Erik Young
+   orcid: 0000-0002-9195-9801
+   affiliation: 1
+ - name: C. Titus Brown
+   orcid: 0000-0001-6001-2677
+   corresponding: true
+   affiliation: 1
+affiliations:
+ - name: University of California, Davis
+   index: 1
+ - name: Woods Hole Oceanographic Institute
+   index: 2
+ - name: Chan-Zuckerberg Biohub
+   index: 3
+ - name:  Pennsylvania State University
+   index: 4
+ - name:  MPI for Evolutionary Biology
+   index: 5
+ - name: Swedish Defence Research Agency (FOI)
+   index: 6
+ - name: National Bioforensic Analysis Center
+   index: 7
+ - name: Washington University in St Louis
+   index: 8
+ - name: No affiliation
+   index: 9
+
+date: 27 Mar 2023
 bibliography: paper.bib
 ---
 
 # Summary
 
-sourmash is a toolbox for creating, comparing, and manipulating MinHash
-sketches of genomic data.
+sourmash is a command line tool and Python library for sketching
+collections of DNA, RNA, and amino acid k-mers for biological sequence
+search, comparison, and analysis [@Pierce:2019]. sourmash's FracMinHash sketching supports fast and accurate sequence comparisons between datasets of different sizes [@gather], including petabase-scale database search [@branchwater]. From release 4.x, sourmash is built on top of Rust and provides an experimental Rust interface.
+
+FracMinHash sketching is a lossy compression approach that represents
+data sets using a "fractional" sketch containing $1/S$ of the original 
+k-mers. Like other sequence sketching techniques (e.g. MinHash, [@Ondov:2015]), FracMinHash provides a lightweight way to store representations of large DNA or RNA sequence collections for comparison and search. Sketches can be used to identify samples, find similar samples, identify data sets with shared sequences, and build phylogenetic trees. FracMinHash sketching supports estimation of overlap, bidirectional containment, and Jaccard similarity between data sets and is accurate even for data sets of very different sizes.
+
+Since sourmash v1 was released in 2016 [@Brown:2016], sourmash has expanded
+to support new database types and many more command line functions.
+In particular, sourmash now has robust support for both Jaccard similarity
+and containment calculations, which enables analysis and comparison of data sets
+of different sizes, including large metagenomic samples. As of v4.4,
+sourmash can convert these to estimated Average Nucleotide Identity (ANI)
+values, which can provide improved biological context to sketch comparisons [@hera2022debiasing].
+
+# Statement of Need
+
+Large collections of genomes, transcriptomes, and raw sequencing data
+sets are readily available in biology, and the field needs lightweight
+computational methods for searching and summarizing the content of
+both public and private collections. sourmash provides a flexible set
+of programmatic functionality for this purpose, together with a robust
+and well-tested command-line interface. It has been used in well over 200
+publications (based on citations of @Brown:2016 and @Pierce:2019) and it continues
+to expand in functionality.
 
-MinHash sketches provide a lightweight way to store "signatures" of
-large DNA or RNA sequence collections, and then compare or search them
-using a Jaccard index.  MinHash sketches can be used to identify samples,
-find similar samples, identify data sets with shared sequences, and
-build phylogenetic trees [@ondov2015fast].
+# Acknowledgements
 
-sourmash provides a command line script, a Python library, and a CPython
-module for MinHash sketches.
+This work is funded in part by the Gordon and Betty Moore Foundation’s
+Data-Driven Discovery Initiative [GBMF4551 to CTB].
 
 # References

pyproject.toml

@@ -13,6 +13,7 @@ version = "4.6.1"
 
 authors = [
   { name="Luiz Irber", orcid="0000-0003-4371-9659" },
+  { name="N. Tessa Pierce-Ward", orcid="0000-0002-2942-5331" },
   { name="Mohamed Abuelanin", orcid="0000-0002-3419-4785" },
   { name="Harriet Alexander", orcid="0000-0003-1308-8008" },
   { name="Abhishek Anant", orcid="0000-0002-5751-2010" },
@@ -33,7 +34,6 @@ authors = [
   { name="Marisa Lim", orcid="0000-0003-2097-8818" },
   { name="Ricky Lim", orcid="0000-0003-1313-7076" },
   { name="Ivan Ogasawara", orcid="0000-0001-5049-4289" },
-  { name="N. Tessa Pierce", orcid="0000-0002-2942-5331" },
   { name="Taylor Reiter", orcid="0000-0002-7388-421X" },
   { name="Camille Scott", orcid="0000-0001-8822-8779" },
   { name="Andreas Sjödin", orcid="0000-0001-5350-4219" },