Added training file for Pseudomonas aeruginosa. Updated links to the …

…NCBI page for the reference genomes used to create training files.

CHANGELOG.md

@@ -2,7 +2,9 @@
 
 ## 3.3.7 - 2024-06-27
 
-- Fixed issue in the PrepExternalSchema module related to the adaptation of small loci (BLASTp would not report the self-alignment). 
+- Fixed issue in the PrepExternalSchema module related to the adaptation of small loci (BLASTp would not report the self-alignment).
+
+- Added training file for *Pseudomonas aeruginosa*.
 
 ## 3.3.6 - 2024-06-12
 

CHEWBBACA/prodigal_training_files/README.md

@@ -1,37 +1,39 @@
 # List of genome assemblies used to create the Prodigal training files
 
-**Acinetobacter baumannii**: [GCF_008632635.1](https://www.ncbi.nlm.nih.gov/assembly/GCF_008632635.1/)
+**Acinetobacter baumannii**: [GCF_008632635.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_008632635.1/)
 
-**Campylobacter jejuni**: [GCF_000304375.1](https://www.ncbi.nlm.nih.gov/assembly/GCF_000304375.1)
+**Campylobacter jejuni**: [GCF_000304375.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000304375.1/)
 
-**Enterococcus faecium**: [GCF_000174395.2](https://www.ncbi.nlm.nih.gov/assembly/GCF_000174395.2)
+**Enterococcus faecium**: [GCF_000174395.2](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000174395.2/)
 
-**Escherichia coli**: [GCF_000008865.2](https://www.ncbi.nlm.nih.gov/assembly/GCF_000008865.2/)
+**Escherichia coli**: [GCF_000008865.2](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000008865.2/)
 
-**Haemophilus influenzae**: [GCF_001856725.1](https://www.ncbi.nlm.nih.gov/assembly/GCF_001856725.1)
+**Haemophilus influenzae**: [GCF_001856725.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_001856725.1/)
 
-**Klebsiella pneumoniae**: [GCF_000240185.1](https://www.ncbi.nlm.nih.gov/assembly/GCF_000240185.1)
+**Klebsiella pneumoniae**: [GCF_000240185.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000240185.1/)
 
-**Legionella pneumophila**: [GCF_000008485.1](https://www.ncbi.nlm.nih.gov/assembly/GCF_000008485.1)
+**Legionella pneumophila**: [GCF_000008485.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000008485.1/)
 
-**Listeria monocytogenes**: [GCF_000196035.1](https://www.ncbi.nlm.nih.gov/assembly/GCF_000196035.1/)
+**Listeria monocytogenes**: [GCF_000196035.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000196035.1/)
 
-**Salmonella enterica enteritidis**: [GCF_000009505.1](https://www.ncbi.nlm.nih.gov/assembly/GCF_000009505.1)
+**Pseudomonas aeruginosa**: [GCF_000006765.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000006765.1/)
 
-**Staphylococcus aureus**: [GCF_000012045.1](https://www.ncbi.nlm.nih.gov/assembly/GCF_000012045.1)
+**Salmonella enterica enteritidis**: [GCF_000009505.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000009505.1/)
 
-**Staphylococcus haemolyticus**: [GCF_000009865.1](https://www.ncbi.nlm.nih.gov/assembly/GCF_000009865.1)
+**Staphylococcus aureus**: [GCF_000012045.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000012045.1/)
 
-**Streptococcus agalactiae**: [GCF_000007265.1](https://www.ncbi.nlm.nih.gov/assembly/GCF_000007265.1/)
+**Staphylococcus haemolyticus**: [GCF_000009865.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000009865.1/)
 
-**Streptococcus canis**: [GCF_900636575.1](https://www.ncbi.nlm.nih.gov/assembly/GCF_900636575.1/)
+**Streptococcus agalactiae**: [GCF_000007265.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000007265.1/)
 
-**Streptococcus dysgalactiae**: [GCF_000317855.1](https://www.ncbi.nlm.nih.gov/assembly/GCF_000317855.1/)
+**Streptococcus canis**: [GCF_900636575.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_900636575.1/)
 
-**Streptococcus equi**: [GCF_000026605.1](https://www.ncbi.nlm.nih.gov/assembly/GCF_000026605.1/)
+**Streptococcus dysgalactiae**: [GCF_000317855.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000317855.1/)
 
-**Streptococcus pneumoniae**: [GCF_000006885.1](https://www.ncbi.nlm.nih.gov/assembly/GCF_000006885.1)
+**Streptococcus equi**: [GCF_000026605.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000026605.1/)
 
-**Streptococcus pyogenes**: [GCF_000006785.2](https://www.ncbi.nlm.nih.gov/assembly/GCF_000006785.2/)
+**Streptococcus pneumoniae**: [GCF_000006885.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000006885.1/)
 
-**Yersinia enterocolitica**: [GCF_000009345.1](https://www.ncbi.nlm.nih.gov/assembly/GCF_000009345.1)
+**Streptococcus pyogenes**: [GCF_000006785.2](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000006785.2/)
+
+**Yersinia enterocolitica**: [GCF_000009345.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000009345.1/)

README.md

@@ -19,7 +19,9 @@ BLAST Score Ratio as proposed by [Rasko DA et al.](http://bmcbioinformatics.biom
 
 ## 3.3.7 - 2024-06-27
 
-- Fixed issue in the PrepExternalSchema module related to the adaptation of small loci (BLASTp would not report the self-alignment). 
+- Fixed issue in the PrepExternalSchema module related to the adaptation of small loci (BLASTp would not report the self-alignment).
+
+- Added training file for *Pseudomonas aeruginosa*.
 
 Check our [Changelog](https://github.com/B-UMMI/chewBBACA/blob/master/CHANGELOG.md) to learn about the latest changes.