Tools and software

Databases, pipelines, and web servers available for analysis of genomic data in NIAGADS and other locations.

Genomics Database

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.

VCPA

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

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.

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.

DASHR

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).

SAVoR

Sequencing Annotation and Visualization of RNA Structures

HAMR

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)

CoRAL

Classification of RNAs by Analysis of Length

ADVP

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.