Tools and software
Databases, pipelines, and web servers available for analysis of genomic data in NIAGADS and other locations.
The NIAGADS GenomicsDB is a searchable annotation resource that provides access to publicly available NIAGADS summary statistics datasets for Alzheimer's Disease and related neuropathologies. These data are curated along with variant and gene annotations and AD-revelant functional genomics datasets, allowing AD researchers to easily identify and interpret interesting genomic regions via interactive search strategies and the NIAGADS genome browser.
SNP/Indel Variant Calling Pipeline and data management tool used for analysis of whole genome and exome sequencing (WGS/WES) for the Alzheimer’s Disease Sequencing Project
VariXam is an aggregated database and a variant browser that shows genomic variants detected on whole-genome/whole-exome sequence (WGS/WES) data from the ADSP.
Alzheimer’s Disease Variants Portal (ADVP) is an integrated, harmonized collection of high-quality and suggestive AD and ADRD genetic association findings across populations curated from the GWAS and related literature.
Functional Annotation of genomic variants in studies of LOAD
Annotations for the WES Release 3 (Atlas Only) Dataset, WGS V1 Dataset. The dataset can be used to annotate single variant association results, or to generate variant groupings by functional annotation for use in SeqMeta and similar tools.
Small non-coding RNAs (sncRNAs) are highly abundant RNAs, typically <100 nucleotides long, that act as key regulators of diverse cellular processes. Although thousands of sncRNA genes are known to exist in the human genome, no single database provides searchable, unified annotation, and expression information for full sncRNA transcripts and mature RNA products derived from these larger RNAs. Here, we present the Database of small human noncoding RNAs (DASHR).
Sequencing Annotation and Visualization of RNA Structures
High-throughput Annotation of Modified Ribonucleotides
SWAN for SV Analysis
A statistical framework for robust detection of genomic structural variants in next-generation sequencing data
Draw + SneakPeak
DNA resequencing analysis workflow (DRAW)
Classification of RNAs by Analysis of Length