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.
NCBI Minute: NCBI Resources for NextGen Sequence Analysis
This webinar covers key NCBI resources that support multiple aspects of next-gen sequence analyses, including quality control, alignment, data visualization and results interpretation. You will also see how to access and apply these resources for both SRA and your own RNA-Seq/DNA-Seq datasets. Whether you’re embarking on your first analysis or already have a background in bioinformatics, you’ll find tools that meet your needs!
NCBI Minute: Running the NCBI PGAP on Your Own Data
You can now download NCBI’s Prokaryotic Genome Annotation Pipeline (PGAP), originally developed at NCBI for RefSeq annotations, and run it on your own machine, a compute farm, or in the Cloud on your own data. PGAP predicts genes on bacterial and archaeal genomes using the same inputs and applications used inside NCBI, and you can now submit genome sequences annotated by your copy of PGAP to GenBank. In this webinar, you will learn how to download PGAP and see an example of how to run it on your own genome assembly to prepare for submission to GenBank. You will also learn how to keep your pipeline up-to-date and running smoothly.
NCBI Minute: Human Population Genetic Data at NCBI
Population variation frequency information can help assess the potential impact of human genetic variants. This webinar introduces you to the population variation datasets at NCBI such as 1000 Genomes, ExAC, GnomAD, and TopMed that are currently included on dbSNP records. You will learn how to find the data, and how you can use this information to interpret and prioritize variants for further study. You will also see a preview a new initiative, the dbGaP Allele Frequency Aggregator (ALFA), that is based on more than 150,000 subjects in 60 dbGaP studies. The initial ALFA public release will include population allele frequencies for more than 500 million known genetic variations and more than 20 million novel variations. We will provide the ALFA data on dbSNP and ClinVar records, on the FTP site for bulk download, and the SPDI APIs for scripting access.