Release notes - April 25, 2021
Genome-wide annotations now available in Annotation Explorer
The Annotation Explorer enables you to interactively explore, query, and study characteristics of an inventory of annotations for the variants called in TOPMed studies.
To support researchers without access to TOPMed studies to perform genome-wide association studies, Seven Bridges collaborated with the TOPMed Data Coordinating Center and generated open access Genome-wide annotations. These are obtained using the Whole Genome Sequencing Annotator software for all combinations of SNVs, including each position in the genome as well as INDELs submitted to dbSNP. To complement the use of Genome-wide annotations, we released the 0.3.0 BETA version of Annotation Explorer. The complete changelog is available in the Annotation Explorer public project description on BioData Catalyst powered by Seven Bridges.
Daily quota for querying is set to 6 TB. Daily quotas reset at midnight Pacific Time. If you wish to try out the Annotation Explorer with the Genome-wide annotations, copy the latest version of Annotation Explorer available in the Annotation Explorer public project to a target project and launch the application. For testing purposes, we recommend that you start by filtering annotations on chromosome 22 and limit the resulting annotation fields and those you want to export to a minimal subset.
The number of users that can use the Annotation Explorer at any given time is limited. Once you start using it, your session will be limited to 3 hours and you will be allowed to use it again in 24 hours.
Learn more about TOPMed Annotation Explorer.
Recently published apps
The following apps were published in CWL1.x:
- SRA Toolkit 2.10.8 - NCBI’s collection of tools and libraries for accessing data in Sequence Read Archives format (SRA).
- SRA Download and Set Metadata - a workflow that allows for downloading full SRA datasets and populating any metadata information that goes with the dataset
- AnnotSV 3.0.7 - structural variant annotation and raking tool.
- IsoformSwitchAnalyzeR 1.12.0 - a tool for differential splicing analysis, it performs statistical identification of the isoform switching while comparing two sample groups.
- DRIMSeq 1.16.1 - performs differential transcript usage (DTU) analyses using Dirichlet-multinomial generalized linear models.
- DEXSeq 1.36.0 - toolkit for testing differential exon usage in comparative RNA-Seq experiments.
- Differential Exon Usage with DEXSeq 1.36.0 - a workflow constructed out of DEXSeq tools, meant for a comprehensive differential splicing analysis.