Tag: Genome

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 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!” →

Introducing the new NCBI Datasets Genomes page

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:

Reference genomes — switch it on to only show reference or representative genomes
Annotated — switch it on to only show annotated genomes
Assembly level — use the assembly level slider to select higher-quality genomes
Year released — use the slider to limit your results to recent genomes

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” →

Retrieve genome data by BioProject using the Datasets command-line tool

You can now retrieve genome data using the NCBI Datasets command-line tool and API by simply providing a BioProject accession. You can go directly from a BioProject accession to genome data even when the BioProject accession is the parent of multiple BioProjects (Figure 1).

Figure 1. Command-lines using BioProject accessions with the datasets command-line tool and sample metadata. Top panel: command-line for downloading genome metadata for the Sanger 25 Genomes Project (PRJEB33226). Middle panel: a portion of the metadata in JSON format for the 25 Genomes Project. Bottom panel: command-line for downloading sequence data and annotation metadata for a component BioProject for the king scallop (PRJEB35331). Continue reading “Retrieve genome data by BioProject using the Datasets command-line tool” →

Genome Workbench Submission Wizard to replace Sequin for prokaryotic and eukaryotic genome submissions in January 2021

If you use Sequin to submit prokaryotic or eukaryotic genome sequences to GenBank, you need to be aware that Sequin will be retired in January 2021. Genome Workbench’s Submission Wizard, which is already available for submitting annotated genomes, will be the submission tool to use for annotated genomes going forward.

Genome Workbench is desktop software that offers a rich set of integrated tools for studying and analyzing genetic data. You can explore and compare data from multiple sources, including the NCBI databases or the your own private data. The Submission Wizard, available since 2019, allows you to prepare submissions of single genomes where all sequences come from the same organism. This interface (Figure 1) is particularly valuable for:

Eukaryotic genomes with annotations, for example those prepared with tbl2asn
Prokaryotic genomes annotated by non-NCBI tools including Prokka and RAST.

Please register to attend our webinar on November 18 to see how to use Genome Workbench to prepare a submission.

(Note: You should continue to submit organelle and viral genomes using BankIt. Please visit the Submission Portal page for information on other submission options.)

Figure 1. Genome Workbench and Submission Wizard. Once the Sequence Editing package is enabled the Submission menu can open the Genome Submission Wizard that prompts you to upload sequence data and presents a tabbed set of forms for entering information about the submission. The Wizard validates the submission and provides editing capabilities for correcting errors. Continue reading “Genome Workbench Submission Wizard to replace Sequin for prokaryotic and eukaryotic genome submissions in January 2021” →

Easily download large amounts of genomic data with NCBI Datasets

Do you need to download a lot of genomic data? Maybe you need all primate reference genomes or maybe you need just a few really big genomes? Prior to the advent of NCBI Datasets, downloading such a large amount of data could be a frustrating and time consuming experience involving failed downloads and writing custom scripts.

NCBI Datasets makes large genome downloads simpler, faster, and more reliable. You don’t have to write a script. You can be sure you get all the data requested. And sharing the data is easier than ever. Figure 1 shows an example data download process using Datasets. Datasets download process

Figure 1. Downloading and processing genomic data using NCBI Datasets. The example shows downloading the set of RefSeq primate assemblies through the Datasets web interface. Since the downloaded files would exceed 15GB, the file comes as a “dehydrated bag” — a small, easily downloaded, zipped file with metadata and links to download the data. You can “rehydrate” the unzipped dehydrated files — fill them with the corresponding data — using the datasets command-line tool.

Continue reading “Easily download large amounts of genomic data with NCBI Datasets” →

Enhanced prokaryote type strain report now with details on needed type strain data

The Prokaryote type strain report provides information on type-strains for over 18,000 species. We revised and expanded the report to make it easier to identify cases where sequencing or establishing type material would have the biggest impact on improving prokaryote taxonomy and accurate identification. These cases include species with designated type strains but without a sequenced type strain assembly and species without designated type material. We hope that the community will prioritize sequencing type strains for the former set of species (Table 1) and establishing a neotype or reftype, where applicable (as defined in Cuifo et al 2018) for the latter set (Table 2).

Other changes from the old format file are detailed in a recent genomes announce post.

Scientific Name	Type material/co-identical strains	Assemblies
Burkholderia ubonensis	CCUG:48852, CIP:1070, …	308
Escherichia albertii	Albert 19982, BCCM/LMG:20976, …	181
Xanthomonas perforans	AATCC:BAA-983, DSM:18975, …	153
Listeria innocua	ATCC:33090, BCCM/LMG:11387, …	106
Streptococcus iniae	ATCC:29178, BCCM/LMG:14520, …	94
Vibrio lentus	CECT:5110, CIP:107166, …	87
Vibrio cyclitrophicus	ATCC:700982, BCCM/LMG:21359, …	83
Pseudomonas coronafaciens	BCCM/LMG:5060, CFPB:2216, …	77
Aliivibrio fischeri	ATCC:7744, BCCM/LMG:4414, …	66
Xanthomonas fragariae	ATCC:33239, BCCM/LMG:708, …	61

Table 1. The top 10 candidate species for sequencing type-strains sorted by the number of assemblies. These have designated type strains but no type strain assembly. We generated the list by sorting by “number of assemblies from type materials per species”, then by decreasing “number of assemblies per taxon”, then filtering out “type materials and coidentical strains” = “na”.

Scientific name	Assemblies
Nostoc linckia	14
Blattabacterium punctulatus	10
Microcystis flos-aquae	10
Microcystis panniformis	9
Microcystis wesenbergii	8
Aphanizomenon flos-aquae	6
Arthrobacter bacterium	6
Denitromonas halophilus	6
Ensifer aridi	6
Methylacidiphilum fumariolicum	6

Table 2. The top 10 candidates for proposing a reftype assembly, or neotype where applicable sorted by the number of assemblies. These species have no designated type strain. We generated the list by selecting for “type materials and coidentical strains” = “na”, “number of assemblies from type materials per species” = 0, and sorting by decreasing “number of assemblies per taxon”, then filtering out Candidatus.

Please contact [email protected] if you want to provide information about missing type-strains.

Expanded average nucleotide identity analysis now available for prokaryotic genome assemblies

As we described in an earlier post, GenBank uses average nucleotide identity (ANI) analysis to find and correct misidentified prokaryotic genome assemblies. You can now access ANI data for the more than 600,000 GenBank bacterial and archaeal genome assemblies through a downloadable report (ANI_report_prokaryotes.txt) available from the genomes/ASSEMBLY_REPORTS area of the FTP site. The README describes the contents of the report in detail. You can use the ANI data to evaluate the taxonomic identity of genome assemblies of interest for yourself.

The new ANI_report_prokaryotes.txt replaces the older ANI_report_bacteria.txt in the same directory. We are no longer updating the ANI_report_bacteria.txt file and will remove it after 31st May 2020.

Important changes coming to prokaryotic Reference and Representative genome assemblies

We are making changes to the set of bacterial and archaeal RefSeq Reference and Representative assemblies in February 2020.

We will reduce the number of Reference assemblies to 15 that have annotation provided by outside experts (Table 1) and re-annotate the 105 other current Reference assemblies using the latest Prokaryotic Genome Annotation Pipeline (PGAP) software. The re-annotated assemblies will lose reference status.
We will reassess and revise the set of Representative assemblies so that there is one assembly per species to better reflect the taxonomic diversity of the RefSeq bacterial and archaeal assemblies.

Continue reading “Important changes coming to prokaryotic Reference and Representative genome assemblies” →

Important changes to the genomes FTP site in February

We have added the latest NCBI Eukaryotic Genome Annotation Pipeline results for the more than 580 species that we annotate to the genomes/refseq directory on the genomes FTP area. As we announced in December, we will stop publishing annotation results to the genus_species directories (example: genomes/Xenopus_tropicalis) on the genomes FTP site effective February 1, 2020. We will also move existing genus_species directories to genomes/archive/old_refseq during the month of February. X_t_assembly Figure 1. The Assembly page for the Xenopus tropicalis UCB Xtro 10.0 (GCF_000004195.4) showing the blue download button. Annotation results such as the RefSeq transcript alignments that can be downloaded from the web page are now also under the genomes/refseq directory on the FTP site. The FTP path to the .bam alignment files is in red.

These FTP changes do not affect the Assembly download function. As always, you can download assembly data using the blue Download button on the web pages (Figure 1).

NCBI on YouTube: Get the most out of NCBI resources with these videos

Check out the latest videos on YouTube to learn how to best use NCBI graphical viewers, SRA, PGAP, and other resources.

Genome Data Viewer: Analyzing Remote BAM Alignment Files and Other Tips

This video shows you how to upload remote BAM files, and succinctly demonstrates handy viewer settings, such as Pileup display options, and highlights the very helpful tooltips in the Genome Data Viewer (GDV). There’s also a brief blog post on the same topic.

Continue reading “NCBI on YouTube: Get the most out of NCBI resources with these videos” →