Next week, NCBI staff will attend AGBT in Marco Island, Florida. On Tuesday, February 25, 2020, three posters from NCBI staff will be on display from 4:40 p.m. – 6:10 p.m. during the Poster Session and Wine Reception in the Banyan and Calusa Ballroom Foyers, Levels 1 and 3. Read on to learn a little bit about what we’ll be presenting.
Poster #514 – “Keeping up with the genomes: updates to NCBI resources for genomic analyses”
As the post-genomic era enters its third decade, data generation, analysis, and discovery show no sign of slowing. The changes and improvements in the technologies in each of these areas have led to an exponential increase in the scale and types of data with which researchers interact.
This poster highlights several of NCBI’s efforts to meet the post-genomic challenges raised in areas of data submission, curation and analysis. Learn about Genome Workbench, a powerful desktop sequence analysis package integrating analysis tools with graphical displays, updates to the suite of command-line alignment tools, the redesigned BLAST results page, recent enhancements to the Genome Data Viewer (GDV), and much more.
Poster #6014 – “De novo assembly of personal genome for cancer mutation detection using multiple whole genome sequencing technologies”
Personal genome assembly provides an unprecedented opportunity to comprehensively study the instability of cancer genome, and accurately pinpoint the full spectrum of the underlined genomics changes that contribute to cancer development, thereby uncovering important genetic markers for cancer diagnostic and drug development. Here we report the reconstruction of genomes of a triple negative breast cancer (TNBC) cell line (HCC1395) and a matched normal cell line (HCC1395BL) using multiple sequencing technologies, including Illumina short reads, 10X Genomics linked reads, PacBio long reads, and Hi-C reads, along with the application of personal genome for cancer somatic variant identification.
Poster #2004 – “Stand-alone PGAP: an NCBI open-source pipeline to annotate prokaryotic genomes”
The NCBI Prokaryotic Genome Annotation Pipeline (PGAP), used to annotate RefSeq prokaryotes assemblies and offered as a service to researchers submitting genome assemblies to GenBank, has become a reliable resource for the prokaryotic community.
We have re-factored PGAP into a stand-alone pipeline that can be executed outside of NCBI on individual computers or in a cloud environment, with the goal of producing annotation that is in line with internal NCBI PGAP and that conforms to GenBank’s standards of quality and format.
We expect that making PGAP portable will accelerate research by providing scientists quality annotations of the genomes they assemble prior to submission, and that it will allow users to iterate over the assembly process until the annotation results demonstrate the quality of the assembly.
Learn about running stand-alone PGAP on your own data in this video https://www.youtube.com/watch?v=pNn_-_46lpI