- Removing Klebsiella_k_locus_variant_reference.gbk.

- Updating docs to reflect this.
- Correcting confidence criteria in docs.

Author: tomdstanton

docs/source/Databases.rst

@@ -187,12 +187,6 @@ The *Klebsiella* K locus primary reference database (``Klebsiella_k_locus_primar
 Synthetic IS-free K locus sequences were generated for K loci for which no naturally occurring IS-free variants have
 been identified to date.
 
-The variants database (``Klebsiella_k_locus_variant_reference.gbk``) comprises full-length annotated sequences for
-variants of the distinct loci:
-
-* IS variants are named as KLN -1, -2 etc e.g. KL15-1 is an IS variant of KL15.
-* Deletion variants are named KLN-D1, -D2 etc e.g. KL15-D1 is a deletion variant of KL15.
-
 .. note::
  KL156-D1 is included in the primary reference database since no full-length version of this locus has been
  identified to date.
@@ -201,7 +195,8 @@ We recommend screening your data with the primary reference database first to fi
 have poor matches or are particularly interested in detecting variant loci you should try the variant database.
 
 .. warning::
- We do not currently recommend using the variant database with Kaptive 3. It is included in the repository for completeness. 
+ The variants database (``Klebsiella_k_locus_variant_reference.gbk``) has been retired as of ``v3.0.0b6`` as it's no
+ longer actively maintained and results can be misleading without additional in depth analysis.
 
 Database versions:
 

docs/source/Interpreting-the-results.rst

@@ -26,16 +26,16 @@ Typeable loci
 The locus was found in a single piece in the query assembly with no genes below the minimum translated identity
 according to the :ref:`locus thresholds <Locus definition>` and:
 
-* no missing genes (as determined by at least 50% nucleotide mapping coverage)
-* no unexpected genes (genes from other loci) inside the locus region of the assembly
+* no missing genes
+* no (non-truncated) unexpected genes (genes from other loci) inside the locus region of the assembly
 
 **OR**
 
 The locus was found in more than one piece in the query assembly with no genes below the minimum translated identity
 according to the :ref:`locus thresholds <Locus definition>` and:
 
-* no more than 1 missing gene  
-* no more than 1 unexpected gene (genes from other loci) inside the locus region of the assembly
+* no less than N% missing genes (default: 50%)
+* no more than N unexpected gene (genes from other loci) inside the locus region of the assembly (default: 1)
 
 These criteria were designed in consideration of the locus definition rules (i.e. that each locus represents a unique set of genes defined at a given minimum translated identity threshold) and following systematic analysis of Kaptive outputs for draft genome assemblies compared against manually confirmed loci determined from matched completed genomes.
 
@@ -57,7 +57,7 @@ Problems
 * ``-`` = genes expected in the locus were not found.
 * ``+`` = extra genes were found in the locus.
 * ``*`` = one or more expected genes was found but with translated identity below the minimum threshold.
-* ``!`` = one or more genes was found but truncated
+* ``!`` = one or more genes was found but truncated.
 
 
 Exploring the other columns

docs/source/Method.rst

@@ -60,6 +60,12 @@ After the best matching locus type has been identified, Kaptive will:
        and each alignment represents the best gene for that part of the contig.
 #. For each remaining gene alignment, the gene is then evaluated.
 
+.. note::
+ You may see multiple entries for the same gene in the gene details columns. This can happen when there are
+ multiple significant alignments for a gene that has been split, either over contigs or by an artefact such as
+ and insertion element. This will be evident by the low percent coverage of the entries, which should all add up
+ to ~100% if they are indeed part of the same gene.
+
 .. _Gene-evaluation:
 
 Gene evaluation

docs/source/Usage.rst

@@ -120,7 +120,7 @@ See database options :ref:`here <Database-options>` and other options::
     -V, --verbose         Print debug messages to stderr
     -v , --version        Show version number and exit
     -h , --help           Show this help message and exit
-    -t , --threads        Number of threads for alignment (default: maximum available CPUs)
+    -t , --threads        Number of threads for alignment (default: maximum available CPUs / 32)
 
 .. _kaptive-convert: