We are excited to announce two improvements to the Read assembly and Annotation Pipeline Tool (RAPT), which allows you to assemble genomic reads for bacterial or archaeal isolates and annotate their genes at the click of a button.
Improved taxonomic assignment
Now RAPT verifies the scientific name you provide with the reads, and corrects it as needed with the Average Nucleotide Identity (ANI) tool, which compares your genome to type strain assemblies in GenBank to place it in the taxonomic tree. So, even if you only have a rough idea of the species you have sequenced, input datasets tailored to your genome will be used for the annotation and you will get the best possible gene set from RAPT. Continue reading “New in RAPT: Better taxonomic assignment and GO annotation”→
Every so often, we gather our most recent videos in one post on the blog, for your convenience. Scroll down – and don’t forget to subscribe to our channel!
Introducing GaPTools for dbGaP Submitters
This video introduces new standalone software called GaPTools, which you can use to check your data before submitting to dbGaP. GaPTools uses the same preliminary validation checks as the dbGaP submission portal.
RefSeq Release 206 is now available. This release includes the following:
Updated human genome Annotation Release 109.20210514
Updated Annotation Release 109.20210514 is an update of NCBI Homo sapiens Annotation Release 109. The annotation report is available here. The annotation products are available in the sequence databases and on the FTP site.
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).
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
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.
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:
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.
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.
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!
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!
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
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.