Read Assembly and Annotation Pipeline Tool (RAPT)

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.

If you are new to RAPT, please visit our wiki page for detailed information.

To download the latest RAPT, run the following command lines at your linux prompt:

~$ curl -sSLo rapt.tar.gz https://github.com/ncbi/rapt/releases/download/v0.2.0/rapt-v0.2.0.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 the two variations of RAPT: Google Cloud Platform (GCP) RAPT and Standalone RAPT. GCP RAPT is designed to run on GCP and is for users with GCP accounts (please note this is different from a gmail account), and Standalone RAPT 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 or Standalone RAPT.