Assemble and annotate your prokaryotic genomes with RAPT

Do you need an easy way to analyze a bacterium you just isolated? The latest version of NCBI’s Read assembly and Annotation Pipeline Tool (RAPT) is a pilot web service for the assembly and gene annotation of public or private Illumina genomic reads sequenced from bacterial or archaeal isolates.

We’ll be giving a webinar on webRAPT on May 19 where you can learn more, but you can test it out now.

Get started with the click of a button

RAPT is simple to use.

1. If you’re working with NIH’s Sequence Read Archive (SRA) and have an SRA accession, enter it in the first box below (Figure 1a) or upload a file of sequencing reads in the second box (Figure 1b).

screenshot of webRAPT submission; enter SRA accession number on the left or upload files on the right
Figure 1. 1a, on the left. Enter an SRA run accession (starting with SRR, DRR or ERR) in the text box on the left if you wish to assemble reads that are already public and press submit. If you are providing a read set that is not in SRA, use the box on the right, shown in 1b. Enter the organism name (genus only or genus species known to NCBI Taxonomy) in the “Organism” field. Click “One file” if all reads for the run are in a single file. This file can contain single-end reads or paired-end reads with reads of a pair adjacent to each other in the file (interleaved). Upload the sequencing reads using the “Choose file” button. Click “Two files” to provide forward and reverse reads from a paired-end library in two separate files. Upload the forward and reverse files using the “Choose Forward Reads File” and “Choose Reverse Reads File” buttons. Then press submit.



2. You’ll get an email when you can download the assembly and its gene annotation.

3. Download and review the results. They include a fasta for the assembly, the Average Nucleotide Identify (ANI) results and the annotation in GenBank and fasta format. Our help documentation has more information on RAPT and the outputs it produces.

New to RAPT?

RAPT is made of two major components: the genome assembler SKESA and the Prokaryotic Genome Annotation Pipeline (PGAP). It produces an annotated genome of quality comparable to RefSeq in a couple of hours. RAPT will also verify that the organism name assigned to the reads is correct using the ANI tool (Figure 2).

The RAPT pipeline. From left to right, the steps are: collect samples, sequence, assemble with SKESA, annotate with PGAP, and analyze.
Figure 2. How RAPT fits in a typical workflow. With RAPT, you are on your way to analyzing your samples as the reads come out of the sequencer!

Watch this short video to learn more.

Run RAPT yourself

Do you prefer to run RAPT on your own local machine or on the cloud? Read our recent blog post and visit our GitHub site to get started.

We would love to hear about your experience using RAPT – web version or command line. Please give us your feedback at You can also email us there if you need more help.

2 thoughts on “Assemble and annotate your prokaryotic genomes with RAPT

  1. Hi Rob – Thank you for your interest in RAPT! We don’t have immediate plans to add an assembler that handles long reads, but will consider your request in the phase of the project. In the meantime, if you are able to assemble your genomes independently, consider using PGAP for the annotation (see

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