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, the taxonomic assignment tool ANI and the Prokaryotic Genome Annotation Pipeline (PGAP).
With RAPT you will:
- assemble your reads into contigs
- assign a scientific name to the assembly
- 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
- estimate the completeness and contamination level of the annotated assembly
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/v0.5.5/rapt-v0.5.5.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.