Tag: Datasets
Missed a few videos on YouTube? Here’s the latest from our channel.
We’re constantly improving the Multiple Sequence Alignment (MSA) Viewer. This video demonstrates several new and popular features, including the ability to change data columns, hide selected rows, analyze polymorphisms, and more.
The National Center for Biotechnology Information (NCBI) has several speakers at the upcoming Biodiversity Genomics Conference from September 27 to October 1, 2021.
Valerie Schneider, head of NCBI’s SeqPlus Program and Deputy Director for Sequence Offerings, will present a poster discussing how NCBI’s new comparative genome research focus will enable researchers to explore all eukaryotic research organisms, find related organisms and support additional organism-specific resources that a specific community may have or wish to develop.
Nuala O’Leary, Product Owner, NCBI Datasets will present the latest developments for Datasets, a beta resource that supports intuitive and flexible access to genome data for a broad range of taxa via a redesigned website and command-line tools.
Adelaide Rhodes, Cloud Subject Matter Expert in Education, will present two case studies that emphasize the ease of navigating the new Datasets website as well as the use of command line tools to speed up data discovery for genes and genomes of interest.
Terence Murphy, Product Owner, NCBI RefSeq will present a new tool for genome providers to identify contamination in newly assembled sequences with high sensitivity, specificity, and performance.
The Biodiversity Genomics Conference brings together a global audience to celebrate achievements in genome sequencing across the eukaryotic tree of life, explore current challenges and solutions, and to develop strategies for sequencing and data sharing in the upcoming decade of biodiversity genomics. NCBI has several programs that support the needs of this scientific research group.
NCBI Datasets introduces species pages and species browser! The species pages summarize taxon information and provide access to genomic data, including reference genomes. For example, see Figure 1, the Nothobranchius furzeri (turquoise killifish) species page.
Figure 1: Nothobranchius furzeri species page. The browse species button will take you to the species browser.
Continue reading “New in NCBI Datasets: Species pages and species browser”
Join us on September 22, 2021 at 12PM eastern time learn to use the datasets command-line tools (datasets and dataformat) to access, filter, download, and format data and metadata for genomes. Through examples from eukaryotes and the SARS-CoV-2 coronavirus, you will see how to use metadata to filter for genome sequences with desired properties such as genomes with high contig N50 values.
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.
The new reference assembly for sheep is now annotated! Assembly ARS-UI_Ramb_v2.0 is made of 142 scaffolds, a drop from 2,640 in the 2017 assembly Oar_rambouillet_v1.0. With a contig N50 of 43 Mb, ARS-UI_Ramb_v2.0 is 15 times more contiguous than the first assembly of the Rambouillet breed.
Annotation Release 104 (AR 104) of ARS-UI_Ramb_v2.0 reflects these improvements. Nearly 200 more coding genes have a 1:1 ortholog in the human genome than in the annotation of Oar_rambouillet_v1.0 (AR 103). The number of coding models annotated as partial is down 35% from 165 to 107, and the number of coding models labeled low quality due to suspected indels or base substitutions in the underlying genomic sequence decreased by 51% (1646 to 796). Based on BUSCO analysis, 99.1% of the models (cetartiodactyla_odb10) are complete in AR 104 versus 98.8% in AR 103. Details of this annotation, including statistics on the annotation products, the input data used in the pipeline and intermediate alignment results, can be found here. Continue reading “Announcing the RefSeq annotation of sheep ARS-UI_Ramb_v2.0!”
Join us on August 18, 2021 at 12PM eastern time for the second webinar on finding data for your non-model research organism. In this webinar, you will learn how to use NCBI’s web resources to get data for a plant species, the black cottonwood. You will see how to find, access, and analyze gene and sequence data from Datasets and other NCBI web resources, as well as sample metadata and gene expression RNA-Seq data from SRA and the SRA Run Selector. You will also see an example that highlights how to use and analyze these data in a typical workflow set up in a Jupyter notebook that uses the NCBI next-gen aligner Magic-BLAST to get relative gene expression levels across samples.
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.
Come visit us virtually to learn about new NCBI data access, tools and best practices at the Bioinformatics Open Science Conference part of the ISMB/ECCB online conference from July 29 – 30, 2021. We will be presenting virtual posters on NCBI resources, offering a Birds of a Feather discussion, and participating in the BOSC (CoFest) following the conference where you can take part in a hands-on evaluation of ElasticBLAST.
NCBI Posters, July 29, 2021, 11:20 – 12:20 PM EDT
All posters will be presented on Thursday afternoon. You can see complete abstracts on the ISMB/ECCB BOSC schedule.
Nuala O’Leary will talk about NCBI Datasets, a new resource for fast, easy access to NCBI sequence data. You will learn about the new interface and new tools to access reference genomes, genes, and orthologs using web-based and programmatic tools.
Adelaide Rhodes will present Open access NCBI cloud resources to accelerate scientific insights where you can learn about recent developments in transferring > 20 petabytes of NCBI Sequence Read Archive (SRA) data to the cloud.
Deacon Sweeney will describe the web RAPT service for assembling and annotating bacterial genomes at the click of a button in RAPT, The Read assembly and Annotation Pipeline Tool: building a prokaryotic genome annotation package for users of all backgrounds.
Roberto Vera Alvarez will talk about best practices for using cloud tools for transcriptomics in his poster Transcriptome annotation in the cloud: complexity, best practices, and cost.
Greg Boratyn will discuss improvements to the BLAST-based short read aligner, Magic-Blast, in Recent improvements in Magic-BLAST 1.6.
Visit Christiam Camacho’s poster ElasticBLAST: Using the power of the cloud to speed up science to get an introduction to ElasticBLAST, a Kubernetes-based approach for high throughput BLAST tasks. Join us following the conference in the CoFest to try out ElasticBLAST yourself and provide input. See the section on the CoFest below and our companion post.
Birds of a Feather, July 29, 2021, 11:20 – 12:20 PM EDT
We will host a Birds of Feather public feedback session on Thursday, where you can provide feedback and participate in discussions on all aspects of NCBI’s new data access options: NCBI Datasets, SRA, BLAST, and the Genome Data Viewer (GDV) — our genome browser for sequence visualization. We welcome your input! Come and see us!
CollaborationFest (CoFest), July 31 – August 1, 2021
The ElasticBlast team will attend the BOSC CoFest following the conference. Sign up to participate on July 31 and August 1 to get an in-depth orientation and opportunity to test the capabilities of ElasticBlast on the Amazon Web Services (AWS) cloud. You do not have to register for the conference to attend the CoFest. See our post on the CoFest for more information.
RefSeq release 207 is now available online, from the FTP site and through NCBI’s Entrez programming utilities, E-utilities.
This full release incorporates genomic, transcript, and protein data available as of July 12, 2021, and contains 285,425,070 records, including 209,035,492 proteins, 39,039,901 RNAs, and sequences from 112,462 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings. Continue reading “RefSeq release 207 is available!”
The updated NCBI Datasets Genomes page now has genome data for all domains of life, including bacterial and viral genomes.
The genomes table (Figure 1) now offers filters for:
In addition, the new Actions column connects you to NCBI’s Genome Data Viewer, BLAST, and Assembly. The Text filter box lets you search by the name of the assembly, species/infraspecies, or submitter.
Figure 1. The new Datasets Genomes page with primate assemblies showing the STATUS switches (reference genomes, annotated); expanded filters section with ASSEMBLY LEVEL and YEAR RELEASED sliding selectors; and the Actions column menu with access to Assembly details, BLAST, the Genome Data Viewer, and Download options. Continue reading “Introducing the new NCBI Datasets Genomes page”
Join us on June 30, 2021 at 12PM eastern time to learn how to use the new NCBI Datasets resource to find and download gene, genome and SARS-CoV-2 sequence and annotation. You will learn how to access these datasets through either the web interface or the new command-line tools that allow you to incorporate these data in your bioinformatic workflows.
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.