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Read Assembly and Annotation Pipeline Tool (RAPT)

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: <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>
• estimate the completeness and contamination level of the annotated assembly<br>

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.