Tag: Read assembly and Annotation Pipeline Tool (RAPT)

Assemble and annotate your prokaryotic genomes with RAPT

Do you need an easy way to analyze a bacterium you just isolated? The Read assembly and Annotation Pipeline Tool (RAPT) is a pilot 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, but you can test it out now.

Try it!

RAPT is simple to use. Provide an SRA accession in the first box below or upload a fasta or fastq file of reads to the second box. Then just press run! You’ll get an email telling you that the job started, and a couple of hours later that the results are available for download.

You can view the jobs you have submitted in the Job List and download and share their results. Please visit the Documentation for more information about RAPT and the outputs it produces, and to learn how to run RAPT on your own machine.

Please give us your feedback at prokaryote-tools@ncbi.nlm.nih.gov.

Continue reading “Assemble and annotate your prokaryotic genomes with RAPT”

May 19 Webinar: Using the new web RAPT service to assemble and annotate prokaryotic genomes

May 19 Webinar: Using the new web RAPT service to assemble and annotate prokaryotic genomes

Join us on May 19, 2021 at 12PM eastern time to learn how to use the new  RAPT pilot service to assemble and annotate public or private Illumina genomic reads sequenced from bacterial or archaeal isolates at the click of a button. RAPT consists of two major components, the genome assembler SKESA and the Prokaryotic Genome Annotation Pipeline (PGAP), and produces an annotated genome of quality comparable to RefSeq in a couple of hours.

  • Date and time: Wed, May 19, 2021 12:00 PM – 12:45 PM EDT
  • 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 webinars playlist on the NLM YouTube channel. You can learn about future webinars on the Webinars and Courses page.

NCBI at CSHL Biology of Genomes, May 11 – 14, 2021

NCBI at CSHL Biology of Genomes, May 11 – 14, 2021

NCBI staff will be presenting virtual posters at the Cold Spring Harbor Laboratory  Biology of Genomes Meeting, May 11 -14, 2021. The posters will cover the following topics: 1) a cloud-ready suite of tools (PGAP, RAPT , and SKESA) for assembling and annotating prokaryotic genomes,  2) Datasets — a new set of services for downloading genome assemblies and annotations, and 3) updates on NCBI RefSeq eukaryotic genome annotation, and the Genome Data Viewer (GDV). Read more below for the full abstracts.

The virtual poster gallery opens Tuesday, May 11 at 9:00 a.m. with dedicated time for poster viewing and discussion at 1:00 to 2:00 p.m. through Slack each day. The poster gallery will be open for entire the conference and remain available for six weeks afterwards.  Continue reading “NCBI at CSHL Biology of Genomes, May 11 – 14, 2021”

New release of the Read Assembly and Annotation Pipeline Tool (RAPT), now 2X faster!

There is a new release of the Read assembly and Annotation Pipeline Tool (RAPT) available from our GitHub site. RAPT is a one-step application for the genome assembly and gene annotation of archaeal and bacterial isolates that can run on your local computer or the Google Cloud Platform (GCP). With this new release, jobs will run twice as fast as with the December release. For example, we have assembled and annotated a Salmonella enterica genome in under an hour on a 16-CPU machine with the new release.
We have also added several new features based on your feedback including:

  1. The –stop-on-errors flag that will stop the process if there evidence from the average nucleotide identity check that there is sample mix-up or contamination by other bacteria.
  2. The ability to accept forward and reverse reads of paired-end runs in separate files. These can be compressed (gzip) files.

Finally, thanks to all who came to our webinar in December and provided their comments! For these who couldn’t join us, you can now view the recording on our YouTube channel.

Contact us at prokaryote-tools@ncbi.nlm.nih.gov with any question and to let us know if you would like to become a beta-tester for RAPT.

NCBI on YouTube: RAPT and BLAST+ on the Cloud, SARS-CoV-2 genome data in Datasets

It’s time we do another roundup of what’s been happening on YouTube!

First up, the NCBI YouTube channel has merged with the NLM YouTube channel. You’ll now be able to find diverse content all on one channel, from tips on using resources to fascinating moments in the history of medicine and more!

Continue reading “NCBI on YouTube: RAPT and BLAST+ on the Cloud, SARS-CoV-2 genome data in Datasets”

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.