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.
If you are new to RAPT, please visit our wiki page for detailed information, and watch a short webinar.
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/v0.4.2/rapt-v0.4.2.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 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 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 Stand-alone RAPT.