Tag: RAPT

Read assembly and Annotation Pipeline Tool (RAPT) is available for use and testing

We are excited to launch a beta version of RAPT, the Read assembly and Annotation Pipeline Tool, a one-step application for the genome assembly and gene annotation of archaeal and bacterial isolates. Start from an Illumina run in SRA or on your local machine and get a fully annotated genome!

A RAPT Docker container includes SKESA, a high-accuracy assembler for short reads, PGAP, the annotation pipeline written in the common workflow language (CWL) and used by RefSeq, and cwltool, the reference implementation for CWL. A RAPT release also includes a set of reference data that are critical for a quality annotation. RAPT can be executed with Docker, Singularity or podman on any local or remote machine meeting basic requirements. For users of the Google Cloud Platform, RAPT can be launched from the Google Shell without configuring a virtual machine in advance.

To learn more about RAPT, register for our upcoming webinar.

Questions? Interest in becoming a beta tester? Contact us!

RAPT is available here.

December 2 Webinar: Using the new Read assembly and Annotation Pipeline Tool (RAPT) to assemble and annotate microbial genomes

December 2 Webinar: Using the new Read assembly and Annotation Pipeline Tool (RAPT) to assemble and annotate microbial genomes

Join us December 2 to learn how to use the Read assembly and Annotation Pipeline Tool (RAPT). With RAPT, you can assemble and annotate a microbial genome right out of the sequencing machine! Provide the short genomic reads or an SRA run on input, and get back the sequence annotated with a complete gene set. The assembly is built with SKESA and annotated with PGAP. In addition, RAPT also verifies the taxonomic assignment of the genome with the Average Nucleotide Identity tool. In this webinar, you will learn how you can run RAPT on your own machine or on the Google Cloud Platform.

  • Date and time: Wed, December 2, 2020 12:00 PM – 12:45 PM EST
  • Register

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.