Category Archives: genome assemblies
Important Update! Changes to ASSEMBLY_REPORTS and GENOME_REPORTS on FTP
Do you currently access genome assembly data through the FTP site? We are consolidating information provided in the ASSEMBLY_REPORTS and GENOME_REPORTS directories on the genomes FTP site to simplify access and ensure that you have the most accurate, up to date, and consistently reported data. The assembly_summary files in the ASSEMBLY_REPORTS directory are gaining information … Continue reading Important Update! Changes to ASSEMBLY_REPORTS and GENOME_REPORTS on FTP
Posted by in assembly, BioProject, Datasets, genome assemblies, NCBI Taxonomy, What's New
Now Available! More Mammalian Cross-Species Alignments in the Comparative Genome Viewer (CGV)
In response to your feedback, we’ve made more whole genome cross-species alignments available in NCBI’s Comparative Genome Viewer (CGV). You can use these alignments to explore genome rearrangements between species. You can also zoom in to analyze regions of conserved gene synteny. There are over 20 new cross-species alignments available, including human-mouse, mouse-rat, human-chimp, human-cattle, … Continue reading Now Available! More Mammalian Cross-Species Alignments in the Comparative Genome Viewer (CGV)
Foreign Contamination Screen (FCS) tool for GenBank submissions
We are excited to introduce a Foreign Contamination Screen (FCS) tool that you can now run yourself, with enhanced contaminant detection sensitivity to improve your genome assemblies and facilitate high-quality data submissions to GenBank. If you submit genome assembly data to GenBank, the FCS tool is for you! What is the FCS tool? FCS, a … Continue reading Foreign Contamination Screen (FCS) tool for GenBank submissions
The post Foreign Contamination Screen (FCS) tool for GenBank submissions appeared first on NCBI Insights.
Posted by in Comparative Genomics Resource (CGR), Genbank, genome assemblies, RefSeq, VecScreen, What's New
Introducing NLM’s new NCBI Datasets genome page!
As part of the NIH Comparative Genomics Resource (CGR) project, NLM’s NCBI Datasets is introducing an all-new modern experience making it easier for you to browse and download genome sequence and metadata, and navigate to tools such as the Genome Data Viewer (GDV) and BLAST. To get started, search NCBI Datasets by assembly accession (e.g., … Continue reading Introducing NLM’s new NCBI Datasets genome page!
The post Introducing NLM’s new NCBI Datasets genome page! appeared first on NCBI Insights.
Introducing NLM’s new NCBI Datasets genome page!
As part of the NIH Comparative Genomics Resource (CGR) project, NLM’s NCBI Datasets is introducing an all-new modern experience making it easier for you to browse and download genome sequence and metadata, and navigate to tools such as the Genome Data Viewer (GDV) and BLAST. To get started, search NCBI Datasets by assembly accession (e.g., … Continue reading Introducing NLM’s new NCBI Datasets genome page!
The post Introducing NLM’s new NCBI Datasets genome page! appeared first on NCBI Insights.
Come see NCBI at the ASM Microbe Conference 2022
The American Society of Microbiology (ASM) Microbe conference is back, and scheduled to take place in-person, June 9th-13th in Washington, D.C. NCBI staff member Dr. Michael Feldgarden will be recognized by ASM with an award for his research. Other NCBI staff will present posters on NCBI resources and will also be available at our booth … Continue reading Come see NCBI at the ASM Microbe Conference 2022
The post Come see NCBI at the ASM Microbe Conference 2022 appeared first on NCBI Insights.
Average Nucleotide Identity (ANI) for assembly validation
Validating genome assemblies submitted to GenBank using ANI based workflow Average Nucleotide Identity (ANI) analysis is a useful tool to verify taxonomic identities in prokaryotic genomes. As part of the NCBI bacterial genome submission process, GenBank performs ANI analyses to compare submitted prokaryotic genome assemblies against reference data generated from type strains. You can learn … Continue reading Average Nucleotide Identity (ANI) for assembly validation
The post Average Nucleotide Identity (ANI) for assembly validation appeared first on NCBI Insights.
Posted by in Genbank, genome assemblies, prokaryotic genome annotation, What's New
RefSeq Release 208 is available!
RefSeq release 208 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 September 7, 2021, and contains 288,903,207 records, including 210,703,648 proteins, 40,213,945 RNAs, and sequences from 113,002 organisms. The release is provided in several directories as a complete dataset … Continue reading RefSeq Release 208 is available!
Sept 22 Webinar: Using NCBI Datasets command-line tools to access data and metadata for genomes
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 … Continue reading Sept 22 Webinar: Using NCBI Datasets command-line tools to access data and metadata for genomes
Posted by in Datasets, GDH, genome assemblies, webinars, What's New
Announcing the RefSeq annotation of sheep ARS-UI_Ramb_v2.0!
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 … Continue reading Announcing the RefSeq annotation of sheep ARS-UI_Ramb_v2.0!