RAPT v0.5.2 - teamcity CI

README.md

@@ -1,18 +1,24 @@
 # Read Assembly and Annotation Pipeline Tool (RAPT)
 
-RAPT is a NCBI pipeline designed for assembling and annotating short genomic sequencing reads obtained from bacterial or archaeal isolates. RAPT consists of two major components, [SKESA](https://github.com/ncbi/SKESA) and [PGAP](https://github.com/ncbi/pgap). SKESA is a *de novo* assembler for microbial genomes based on DeBruijn graphs. PGAP is a prokaryotic genome annotation pipeline that combines *ab initio* gene prediction algorithms with homology-based methods. RAPT takes an SRA run or a fasta or fastq file of Illumina reads as input and produces an assembled and annotated genome. 
+RAPT is an NCBI pipeline designed for **assembling and annotating short genomic sequencing reads** obtained from **bacterial or archaeal isolates** *de novo*. It takes an SRA run or a fasta or fastq file of Illumina reads as input and produces an assembled and annotated genome of **quality comparable to RefSeq** in a couple of hours. 
+RAPT consists of three major components, the genome assembler [SKESA](https://github.com/ncbi/SKESA), the taxonomic assignment tool [ANI](https://pubmed.ncbi.nlm.nih.gov/29792589/) and the Prokaryotic Genome Annotation Pipeline ([PGAP](https://github.com/ncbi/pgap)).
+
+With RAPT you will:<br>
+* **assemble your reads** into contigs<br>
+* **assign a scientific name** to the assembly<br>
+* **predict coding and non-coding genes** *de novo*, including anti-microbial resistance (AMR) genes and virulence factors, based on expert-curated data such as hidden Markov models and conserved domain architectures<br>
 
 If you are new to RAPT, please visit our [wiki page](https://github.com/ncbi/rapt/wiki) for detailed information, and watch a [short webinar](https://www.youtube.com/watch?v=7trM1pKAVXQ).
 
-![RAPT](RAPT_context4.png)
+![RAPT](RAPT_context_Apr2022.png)
 
 To use the latest version, download the RAPT command-line interface with the following commands:
 ```
-~$ curl -sSLo rapt.tar.gz https://github.com/ncbi/rapt/releases/download/v0.5.1/rapt-v0.5.1.tar.gz
+~$ curl -sSLo rapt.tar.gz https://github.com/ncbi/rapt/releases/download/v0.5.2/rapt-v0.5.2.tar.gz
 ~$ tar -xzf rapt.tar.gz && rm -f rapt.tar.gz
 ```
 
 
-There should be two scripts in your directory now, `run_rapt_gcp.sh` and `run_rapt.py`, corresponding to two variations of RAPT:  Google Cloud Platform (GCP) RAPT and Standalone RAPT. [GCP RAPT](https://github.com/ncbi/rapt/wiki/GCP%20RAPT%20In-depth%20Documentation%20and%20Examples) is designed to run on GCP and is for users with GCP accounts (please note this is different from a gmail account), while [Stand-alone RAPT](https://github.com/ncbi/rapt/wiki/Standalone%20RAPT%20In-depth%20Documentation%20and%20Recommendations) can run on any computing environments meeting a few pre-requisites.
+There should be two scripts in your directory now, `run_rapt_gcp.sh` and `run_rapt.py`, corresponding to two variations of RAPT:  Google Cloud Platform (GCP) RAPT and Standalone RAPT. [GCP RAPT](https://github.com/ncbi/rapt/wiki/GCP_RAPT_doc) is designed to run on GCP and is for users with GCP accounts (please note this is different from a gmail account), while [Stand-alone RAPT](https://github.com/ncbi/rapt/wiki/Standalone_RAPT_doc) can run on any computing environments meeting a few pre-requisites.
 
-For instructions on running RAPT, please go to their respective documentation pages: [GCP RAPT](https://github.com/ncbi/rapt/wiki/GCP%20RAPT%20In-depth%20Documentation%20and%20Examples) or [Stand-alone RAPT](https://github.com/ncbi/rapt/wiki/Standalone%20RAPT%20In-depth%20Documentation%20and%20Recommendations).
+For instructions on running RAPT, please go to their respective documentation pages: [GCP RAPT](https://github.com/ncbi/rapt/wiki/GCP_RAPT_doc) or [Stand-alone RAPT](https://github.com/ncbi/rapt/wiki/Standalone_RAPT_doc).

dist/CHANGELOG.md

@@ -1,3 +1,7 @@
+### Release v0.5.2
+* PGAP at 2022-04-14.build6021
+* Add `--auto-correct-tax` switch
+
 ### Release v0.5.1
 * PGAP at 2022-02-10.build5872
 

dist/README.txt

@@ -1,4 +1,4 @@
-Read Assembly and Annotation Pipeline Tool (RAPT) v0.5.1
+Read Assembly and Annotation Pipeline Tool (RAPT) v0.5.2
 
 RAPT is a NCBI pipeline designed for assembling and annotating Illumina genome sequencing reads obtained from bacterial or archaeal isolates. RAPT consists of two major NCBI components, SKESA and PGAP. SKESA is a de-novo assembler for microbial genomes based on DeBruijn graphs. PGAP is a prokaryotic genome annotation pipeline that combines ab initio gene prediction algorithms with homology based methods. RAPT takes an Illumina SRA run or a fasta file as input and produces an assembled and annotated genome. 
 

dist/release-notes.txt

@@ -1,9 +1,9 @@
-RELEASE: v0.5.1
-DATE: 03-18-2022
-BUILD: rapt-37347638
+RELEASE: v0.5.2
+DATE: 05-04-2022
+BUILD: rapt-38092134
 SKESA: 2.5.0
-PGAPX: 2022-02-10.build5872
+PGAPX: 2022-04-14.build6021
 
 DESCRIPTION:
 
-This release updates PGAP to 2022-02-10.build5872
+This release updates PGAP to 2022-04-14.build6021, and implemented --auto-correct-tax switch: when specified, in the case that the genome sequence is misassigned or contaminated and ANI predicts an organism with HIGH confidence, the system will use the predicted organism for PGAP instead of the one provided by the user.