docs: update AlleleCall page.

Author: rfm-targa

CHEWBBACA/docs/_static/custom.css

@@ -13,5 +13,4 @@ div.wy-side-nav-search, div.wy-nav-top {
 table.align-center {
     margin-left: auto;
     margin-right: auto;
-    text-align: center;
 }

CHEWBBACA/docs/user/getting_started/important_notes.rst

@@ -12,8 +12,7 @@ Important Notes
 - chewBBACA defines an allele as a complete Coding DNA Sequence (CDS), with start and stop codons
   according to the `NCBI genetic code table 11 <http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi>`_
   (identified using `Prodigal <https://github.com/hyattpd/prodigal/releases/>`_ for chewBBACA<=3.2.0 and
-  `Pyrodigal <https://github.com/althonos/pyrodigal>`_ for chewBBACA>=3.3.0, but with the option to provide FASTA
-  files with CDSs). It will automatically exclude any allele for which the DNA sequence does not contain start or stop
+  `Pyrodigal <https://github.com/althonos/pyrodigal>`_ for chewBBACA>=3.3.0). It will automatically exclude any allele for which the DNA sequence does not contain start or stop
   codons and for which the length is not multiple of three. Alleles that contain ambiguous bases are also excluded.
 - Make sure that your FASTA files are UNIX format. If they were created in Linux or MacOS
   systems they should be in the correct format, but if they were created in Windows systems,

CHEWBBACA/docs/user/getting_started/installation.rst

@@ -8,15 +8,15 @@ Install the latest released version using `conda <https://anaconda.org/bioconda/
 
 ::
 
-	conda create -c bioconda -c conda-forge -n chewie "chewbbaca=3.3.9"
+	conda create -c bioconda -c conda-forge -n chewie "chewbbaca=3.3.10"
 
 If you're having issues installing chewBBACA through conda, please verify that you are using
 conda>=22.11, and enable the libmamba solver, which might speed up the installation process.
 You can also install `mamba <https://mamba.readthedocs.io/en/latest/index.html>`_ and run the following command:
 
 ::
 
-	mamba create -c bioconda -c conda-forge -n chewie "chewbbaca=3.3.9"
+	mamba create -c bioconda -c conda-forge -n chewie "chewbbaca=3.3.10"
 
 .. important::
 	We strongly recommend that users install and use BLAST 2.9.0+ with chewBBACA<=3.3.2. Please open an
@@ -54,15 +54,15 @@ Other dependencies
 
 * `BLAST >=2.9.0 <https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/>`_ (we recommend using BLAST 2.9.0+)
 * `Prodigal >=2.6.3 <https://github.com/hyattpd/prodigal/releases/>`_ (for chewBBACA <3.3.0)
-* `MAFFT >=7.505 <https://mafft.cbrc.jp/alignment/software/>`_ (for schema evaluation only)
-* `FastTree >=2.1.11 <http://www.microbesonline.org/fasttree/>`_ (for allele calling evaluation only)
+* `MAFFT >=7.505 <https://mafft.cbrc.jp/alignment/software/>`_ (used by the SchemaEvaluator module only)
+* `FastTree >=2.1.11 <http://www.microbesonline.org/fasttree/>`_ (used by the AlleleCallEvaluator module only)
 
 .. important::
 	Installation through conda should take care of all dependencies. If you install through
 	pip you need to ensure that you have BLAST, MAFFT, FastTree and Prodigal (for chewBBACA <3.3.0)
 	installed and added to the PATH.
 
-The reports generated by the SchemaEvaluator and AlleleCallEvaluator modules use the `React <https://react.dev/>`_ library and the following JavaScript packages:
+The reports generated by the SchemaEvaluator and AlleleCallEvaluator modules use the `React <https://react.dev/>`_ library and the following JavaScript (JS) packages:
 
   - `Material UI <https://www.npmjs.com/package/@mui/material>`_ for most of the components.
   - `MUI-Datatables <https://www.npmjs.com/package/mui-datatables>`_ for datatables components.
@@ -73,5 +73,4 @@ The reports generated by the SchemaEvaluator and AlleleCallEvaluator modules use
   - `Monaco Editor for React <https://www.npmjs.com/package/@monaco-editor/react>`_ for the read-only code editor that displays the DNA and Protein sequences.
   - `react-markdown <https://www.npmjs.com/package/react-markdown>`_ and `remark-gfm <https://www.npmjs.com/package/remark-gfm>`_ to render markdown.
 
-.. note::
-	You do not need to install the JS packages. chewBBACA includes JS bundles that are added to the report directory and are used by the browser.
+You do not need to install these JS packages. chewBBACA includes `JS bundles <https://github.com/B-UMMI/chewBBACA/tree/master/CHEWBBACA/report_template_components/src/bundles>`_ that are added to the report directory and are used by the browser.

CHEWBBACA/docs/user/getting_started/overview.rst

@@ -25,8 +25,8 @@ The main processes available in chewBBACA are represented in the following workf
 - Steps labelled 1: Schema creation from genome assemblies or coding sequences in FASTA format.
 - Steps labelled 2: Adaptation of external schemas for usage with chewBBACA.
 - Steps labelled 3: Upload, download, and synchronize schemas from `Chewie-NS <https://chewbbaca.online/>`_.
-- Steps labelled 4: Perform allele calling to determine allelic profiles.
-- Steps labelled 5: Compute the core genome based on allele calling results.
+- Steps labelled 4: Perform allele calling to determine the allelic profiles of strains of interest.
+- Steps labelled 5: Determine the set of loci that constitute the core genome based on allele calling results.
 - Steps labelled 6: Annotate schema loci based on UniProt data.
 - Steps labelled 7: Evaluate schemas and explore loci diversity through an interactive report.
 - Steps labelled 8: Evaluate allele calling results through an interactive report.

CHEWBBACA/docs/user/getting_started/useful_links.rst

@@ -5,8 +5,6 @@ Useful links
   Chewie-NS allows chewBBACA users to download and update cg/wgMLST schemas,
   allowing the easy sharing of results, while ensuring the reproducibility and
   consistency of these steps.
-- Use `BBACA gitter <https://gitter.im/BBACA/Lobby>`_ if you have any pressing
-  question. Chat can be faster and better than email for troubleshooting purposes.
 - A ready to use `docker image <https://hub.docker.com/r/ummidock/chewbbaca>`_
   automatically built from the latest version of chewBBACA in Ubuntu 22.04.
 - chewBBACA is available as a `Galaxy module <https://toolshed.g2.bx.psu.edu/repository?repository_id=88fd7663075eeae9&changeset_revision=093352878303>`_.

CHEWBBACA/docs/user/help_support/contacts.rst

@@ -2,10 +2,8 @@ Contacts
 ========
 
 chewBBACA is developed by the `Molecular Microbiology and Infection Unit (UMMI) 
-<http://im.fm.ul.pt>`_ at the 
-`Instituto de Medicina Molecular João Lobo Antunes 
-<https://imm.medicina.ulisboa.pt/>`_ and `Faculdade de Medicina, Universidade de Lisboa 
-<https://www.medicina.ulisboa.pt/>`_.
+<http://im.fm.ul.pt>`_ at the `Lisbon School of Medicine, University of Lisbon 
+<https://www.medicina.ulisboa.pt/en>`_.
 
-For any issues contact the development team at [email protected] or 
-open an issue at the chewBBACA Github `repository <https://github.com/B-UMMI/chewBBACA>`_.
+For any requests or to report issues contact the development team at [email protected] or 
+open an `issue <https://github.com/B-UMMI/chewBBACA/issues>`_ on Github.

CHEWBBACA/docs/user/help_support/faq.rst

@@ -4,7 +4,7 @@ FAQ
 What strains should I use for :doc:`Schema Creation </user/modules/CreateSchema>`?
 ..................................................................................
 The set of genome assemblies used for schema creation should be carefully selected to avoid
-the inclusion of spurious loci in the schema seed that result from low quality assemblies
+the inclusion of spurious loci in the schema seed that result from low quality genome assemblies
 (e.g.: genome assemblies resulting from low quality sequencing data, highly fragmented genome
 assemblies, genome assemblies with many frameshifted proteins, genome length too large or too
 small). A set of high quality genome assemblies, ideally complete genomes, that capture the
@@ -23,7 +23,7 @@ chewBBACA accepts input files with the following file extensions: ``.fasta``, ``
 
 I ran all the steps and my cgMLST loci size is smaller than traditional MLST...does this even work?
 ...................................................................................................
-In order to have a robust definition of a cgMLST schema for a given bacterial species, a set
+In order to have a robust definition of a cgMLST schema, a set
 of representative strains of the diversity of a given species should be selected. Furthermore,
 since cgMLST schema definition is based on pre-defined thresholds, only when a sufficient number
 of strains have been analyzed can the cgMLST schema be considered stable. This number will always
@@ -100,8 +100,10 @@ At the moment:
 - *Enterococcus faecium*
 - *Escherichia coli*
 - *Haemophilus influenzae*
+- *Klebsiella pneumoniae*
 - *Legionella pneumophila*
 - *Listeria monocytogenes*
+- *Pseudomonas aeruginosa*
 - *Salmonella enterica enteritidis*
 - *Staphylococcus aureus*
 - *Staphylococcus haemolyticus*
@@ -117,15 +119,17 @@ get them `here <https://github.com/B-UMMI/chewBBACA/tree/master/CHEWBBACA/prodig
 
 My favorite species has no training file. What can I do?
 ........................................................
-You can propose a new one to be added to the repository or create your own training files.
-To create a training file make sure you have Prodigal installed and run the following command:
+You can propose a new one to be added to the repository or create your own.
+To create a training file make sure you have Prodigal installed and adapt the following command:
 
 ::
 
 	prodigal -i myGoldStandardGenome.fna -t myTrainedFile.trn -p single
 
+The `Prodigal wiki <https://github.com/hyattpd/prodigal/wiki/Gene-Prediction-Modes#training-mode>`_
+includes more detailed information about how to create a training file.
+
 How should I cite chewBBACA?
 ............................
-If you use chewBBACA, please cite:
 
-Silva M, Machado MP, Silva DN, Rossi M, Moran-Gilad J, Santos S, Ramirez M, Carriço JA. 2018. chewBBACA: A complete suite for gene-by-gene schema creation and strain identification. Microb Genom 4:000166. doi:10.1099/mgen.0.000166
+Please refer to the Citation section in the :doc:`Overview </user/getting_started/overview>` page.