GenBank release 233.0 (8/21/2019) is now available on the NCBI FTP site. This release has 6.26 terabases and 1.65 billion records.
The release has 213,865,349 traditional records containing 366.7 billion base pairs of sequence data. There are also 1.07 billion WGS records containing 5.6 trillion base pairs of sequence data, 331.3 million bulk-oriented TSA records containing 294.7 trillion base pairs of sequence data, and 26 million bulk-oriented TLS records containing 10.5 billion base pairs of sequence data.
NCBI’s Genetic Relationship and Fingerprinting (GRAF) tool is a quality assurance tool that can quickly find duplicates and closely related subjects in your data using SNP genotypes.
The population tool GRAF-pop included in GRAF computes subject ancestries using genotypes and normalizes ancestry prediction in large datasets collected across different genotyping platforms, making it possible to generate population frequency based on more than a million dbGaP samples.
Who can use this?
GRAF is a tool for researchers; it is not designed to assess an individual’s ancestry or to find relatives.
You can use this tool against your own large datasets with results generated within hours or minutes, even when there is a very high genotype missing rate to the order of 99%. This tool can check genotype datasets obtained using different chips or platforms, plotting them in the same picture for comparison purposes.
We’ve just released a new version of Magic-BLAST with several new, user-driven enhancements like:
- Nanopore sequence alignment
- Improved multithreading performance
- Support for the new BLAST database version, BLASTDBv5, that allows you to limit your search by taxonomy
- More reliable placements of reads
The new executables are available on the NCBI FTP site.
A new paper (PMID: 31345161), published in July 2019 by BMC Bioinformatics, presents the usage accuracy of Magic-BLAST.
Magic-BLAST aligns next generation DNA- and RNA-Seq sequencing reads. Read more about the latest version of Magic-BLAST in the release notes.
You may know . . .
- We offer expert-authored, peer-reviewed chapters on more than 750 genetic disorders.
- Our standardized format enables busy clinicians to readily find the information they need.
- Molecular genetic testing strategies are presented in the context of clinical care and genetic counseling implications.
- Tables link specific molecular genetic information to entries in OMIM (Online Mendelian Inheritance in Man), ClinVar, and genomic databases.
- Resource lists connect families to information and support.
- Links to actionable information for clinicians to find available Clinical Trials and genetic tests in the NIH’s Genetic Testing Registry (GTR).
- Chapters are continually updated to reflect changes in clinically relevant information, such as test availability and treatment protocols.
But do you also know . . .
- You can volunteer to create a GeneReviews® chapter in your area of expertise. Start by reading the information for prospective authors.
- Our Educational Materials, designed for health care professionals of varying experience with clinical genetics, augment our glossary to clarify genetics concepts.
- For genetics professionals, we summarize the latest information on:
- Imprinting errors and uniparental disomy (UPD) not detectable by sequence analysis
- Disorders caused by nucleotide repeat expansions/contractions
- Disorders with highly homologous gene family members or pseudogenes
- Founder variant tables compile, for the first time in one place, data to inform testing recommendations and clinical decision making for disorders more common in Finnish, Ashkenazi Jewish, Inuit, Yup’ik, Cree/Ojibway, and Navajo
- A succinct, one-stop information page on direct-to-consumer genetic testing gives medical professionals information they need in order to advise patients who have pursued testing on their own.
Check our What’s New page for weekly new and updated postings.
Recently, the NCBI Eukaryotic Genome Annotation Pipeline has released new annotations in RefSeq for the following organisms:
As you may know, we have been offering a new BLAST results (Figure 1) as a test page since April. In response to your positive reception and after incorporating many improvements that you suggested, we made the new results the default today, August 1, 2019.
You will still be able to access to the traditional results for a several months. This will provide you additional time if you need it to adjust your workflows or teaching materials to the new display.