We’ve just released a new version (1.6.0) of Magic-BLAST, the BLAST-based next-gen alignment tool, with these improvements:
Usage reporting — you can help improve Magic-BLAST by sharing limited information about your search. The BLAST User Manual has details on the information collected, how it is used, and how to opt-out.
Magic BLAST can access NCBI SRA next-gen reads from the cloud when you use the -sra or -sra_batch options. See the Magic-BLAST cookbook for more details.
NCBI taxonomy IDs are reported in SAM output if they are present in the target BLAST database.
You can get unaligned reads reported separately from the aligned ones by using the -out_unaligned <file name> option. You can also select the format ( SAM, tabular, or FASTA) with the -unaligned_fmt option. The default format is the same as one for the main report .
We are happy to announce an updated bacterial and archaeal representative genome collection! We have selected 13,835 among 214,000 prokaryotic RefSeq assemblies to represent their respective species. The collection has increased by 6% since December 2020. About 950 species are represented for the first time, 476 species are represented by a better assembly, and 170 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment.
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.
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 firstname.lastname@example.org.
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
During the COVID-19 pandemic, it is critical to collect descriptive information about the provenance and attributes of SARS-CoV-2 genomic samples so that the course of the virus may be tracked and analyzed. The NCBI Submission Portal now includes a dedicated BioSample submission package to help further improve the quality and richness of submitted SARS-CoV-2 sample metadata. The SARS-CoV-2 clinical or host-associated package presents a framework and standardized fields for submitters to provide attributes considered useful for the rapid analysis and surveillance of SARS-CoV-2 clinical and host-associated cases. For example, mandatory attributes include collection date and geographic location, while suggested but optional attributes include date of SARS-CoV-2 vaccination, vaccine received, and host disease outcome.
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.
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Add Preprint Citations in My Bibliography
The National Institutes of Health encourages investigators to post preprints to public repositories in order to speed the dissemination and enhance the rigor of their work. This video demonstrates how to add preprint citations to My Bibliography.
The NCBI Assembly database now provides sequence and metadata for more than 1 million genome assemblies from over 85,000 different species.
Assembly crossed the 1 million genome assemblies milestone on Sunday, April 18, 2021 (Figure 1).
Figure 1. Assembly status and growth. More than 1 million assemblies are now searchable through the NCBI web site (top panel). The number of genome assemblies at NCBI has accelerated rapidly in the past decade.