EBIvariation/eva-tools

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Java
License
Apache License 2.0
Created over 8 years ago
Updated 6 months ago

EBIvariation/eva-tools

EBIvariation

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Tools compatible with the infrastructure of the European Variation Archive pipeline

vcf-validator

Validation suite for Variant Call Format (VCF) files, implemented using C++11

CMAT

ClinVar Mapping and Annotation Toolkit

Jupyter Notebook

eva-ws

European Variation Archive REST web services API

variant-remapping

The pipeline for remapping VCF variants between two arbitrary FASTA assemblies.

eva-pipeline

Genomic variation pipeline for the European Variation Archive, implemented using Spring Batch

eva-web

Web front-end for the European Variation Archive

examples

Examples to be used as reference in other projects

contig-alias

Service to provide synonyms of chromosome/contig identifiers

eva-accession

EVA non-human variant accessioning service

variation-commons

Library of core components used by multiple EBI Variation projects

trait-curation

A web application for manual curation of trait-to-ontology mappings, including provenance and integration with EBI SPOT stack.

metadata-ws

Generic REST API for submission metadata objects (usable by AMP T2D, EGA and EVA)

eva-submission

Components that connect and automate main tasks in the EVA submission workflow

eva-assembly-ingestion

Automation for ingesting a new assembly for a species

eva-seqcol

Java implementation of the sequence collection specification to represent INSDC assemblies

eva-v2

This repository has now been split for better modularization. Please see eva-pipeline (develop branch), eva-tools and eva-ws.

opentargets-pharmgkb

Pipeline to provide evidence strings for Open Targets from PharmGKB

Jupyter Notebook