From 5e2b90387db98a8ee5f173cde6e175da9f324d18 Mon Sep 17 00:00:00 2001 From: rfm-targa Date: Thu, 27 Jun 2024 12:15:45 +0100 Subject: [PATCH] Added training file for Pseudomonas aeruginosa. Updated links to the NCBI page for the reference genomes used to create training files. --- CHANGELOG.md | 4 +- .../Pseudomonas_aeruginosa.trn | Bin 0 -> 558392 bytes CHEWBBACA/prodigal_training_files/README.md | 38 +++++++++--------- README.md | 4 +- 4 files changed, 26 insertions(+), 20 deletions(-) create mode 100644 CHEWBBACA/prodigal_training_files/Pseudomonas_aeruginosa.trn diff --git a/CHANGELOG.md b/CHANGELOG.md index c8f7299c..142e0a4c 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/CHEWBBACA/prodigal_training_files/Pseudomonas_aeruginosa.trn 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b/CHEWBBACA/prodigal_training_files/README.md index c91fc770..cb37ac76 100644 --- a/CHEWBBACA/prodigal_training_files/README.md +++ b/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/) diff --git a/README.md b/README.md index 46a97d15..7fe1ab8f 100644 --- a/README.md +++ b/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.