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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 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 SRA run or a fasta or fastq file of Illumina reads as input and produces an assembled and annotated genome.
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RAPT is implemented as a Docker image for maximal portability. The image is hosted at dockerhub and is publicly accessible. Command line interface scripts are provided on github for download. Copy and paste the following command lines at your linux prompt to download and extract the files:
curl -sSLo rapt.tar.gz https://github.com/ncbi/rapt/releases/download/v0.5.5/rapt-v0.5.5.tar.gz
tar -xzf rapt.tar.gz && rm -f rapt.tar.gz
You should now have two scripts in your directory: run_rapt_gcp.sh and run_rapt.py. If you have a Google Cloud Platform account, you can run GCP RAPT with run_rapt_gcp.sh. Otherwise you may use the run_rapt.py to run stand-alone RAPT on any computer as long as it meets a set of minimal requirements.
- GCP RAPT: For users with a Google Cloud Platform account.
- Stand-alone RAPT: For users with computers meeting a set of minimal requirements.
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