Repositories list

• variant-remapping

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

  Python

  •

  Apache License 2.0

  •7•5•6•0•Updated Jan 27, 2025Jan 27, 2025

• CMAT

  Public
  ClinVar Mapping and Annotation Toolkit

  Jupyter Notebook

  •

  Apache License 2.0

  •10•19•59•1•Updated Jan 27, 2025Jan 27, 2025

• eva-submission

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

  Python

  •

  Apache License 2.0

  •7•1•0•5•Updated Jan 24, 2025Jan 24, 2025

• opentargets-pharmgkb

  Public
  Pipeline to provide evidence strings for Open Targets from PharmGKB

  Jupyter Notebook

  •

  Apache License 2.0

  •1•1•11•1•Updated Jan 22, 2025Jan 22, 2025

• eva-common-pyutils

  Public
  EBI EVA - Common Python Utilities

  Python

  •

  Apache License 2.0

  •6•0•0•0•Updated Jan 21, 2025Jan 21, 2025

• eva-accession

  Public
  EVA non-human variant accessioning service

  Java

  •

  Apache License 2.0

  •12•4•0•5•Updated Jan 21, 2025Jan 21, 2025

• eva-assembly-ingestion

  Public
  Automation for ingesting a new assembly for a species

  Python

  •

  Apache License 2.0

  •4•1•0•0•Updated Jan 20, 2025Jan 20, 2025

• eva-submission-ws

  Public
  Web services for EVA Submissions

  Java

  •

  Apache License 2.0

  •4•0•0•1•Updated Jan 20, 2025Jan 20, 2025

• accession-commons

  Public
  Generic library for accessioning any type of object

  Java

  •

  Apache License 2.0

  •12•0•0•2•Updated Jan 15, 2025Jan 15, 2025

• eva-sub-cli

  Public
  EVA Submission Command Line Interface for Validation

  HTML

  •

  Apache License 2.0

  •4•0•0•0•Updated Jan 14, 2025Jan 14, 2025

• eva-web

  Public
  Web front-end for the European Variation Archive

  JavaScript

  •10•5•0•1•Updated Jan 6, 2025Jan 6, 2025

• vcf-validator

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

  C++

  •

  Apache License 2.0

  •41•133•4•5•Updated Dec 18, 2024Dec 18, 2024

• eva-tasks

  Public
  Code used to to perform tasks or one of analysis.

  Jupyter Notebook

  •

  Apache License 2.0

  •6•0•0•1•Updated Dec 16, 2024Dec 16, 2024

• eva-pipeline

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

  Java

  •

  Apache License 2.0

  •24•6•0•8•Updated Dec 3, 2024Dec 3, 2024

• eva-ws

  Public
  European Variation Archive REST web services API

  Java

  •

  Apache License 2.0

  •21•6•0•10•Updated Oct 29, 2024Oct 29, 2024

• eva-tools

  Public
  Tools compatible with the infrastructure of the European Variation Archive pipeline

  Java

  •

  Apache License 2.0

  •13•1•0•9•Updated Oct 23, 2024Oct 23, 2024

• metadata-ws

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

  Java

  •

  Apache License 2.0

  •9•1•0•2•Updated Aug 26, 2024Aug 26, 2024

• ega-accession

  Public
  EGA accessioning service

  Java

  •6•0•0•3•Updated Aug 26, 2024Aug 26, 2024

• web-prototype

  Public
  Prototypes for new website components in React

  JavaScript

  •

  Apache License 2.0

  •3•0•0•0•Updated Jul 30, 2024Jul 30, 2024

• eva-seqcol

  Public
  Java implementation of the sequence collection specification to represent INSDC assemblies

  Java

  •

  Apache License 2.0

  •5•1•10•3•Updated May 22, 2024May 22, 2024

• contig-alias

  Public
  Service to provide synonyms of chromosome/contig identifiers

  Java

  •

  Apache License 2.0

  •11•4•10•10•Updated Mar 19, 2024Mar 19, 2024

• amp-t2d-property-registry

  Public
  Registry service for AMP T2D properties

  Java

  •

  Apache License 2.0

  •3•0•0•6•Updated Feb 22, 2024Feb 22, 2024

• amp-t2d-kb-test

  Public
  Java

  •2•0•0•2•Updated Jan 22, 2024Jan 22, 2024

• eva-common-groovyutils

  Public
  EBI EVA - Common Groovy Utilities

  Groovy

  •

  Apache License 2.0

  •1•0•0•1•Updated Nov 4, 2023Nov 4, 2023

• eva-vcf-merge

  Public
  Tool for merging large sets of VCF files

  Python

  •

  Apache License 2.0

  •3•0•0•0•Updated Oct 30, 2023Oct 30, 2023

• covid19dp-submission

  Public
  Covid-19 data portal submissions

  Python

  •

  Apache License 2.0

  •4•0•0•0•Updated Oct 30, 2023Oct 30, 2023

• variation-commons

  Public
  Library of core components used by multiple EBI Variation projects

  Java

  •

  Apache License 2.0

  •16•2•0•3•Updated Oct 26, 2023Oct 26, 2023

• eva-internal-pyutils

  Public
  Python utilities used for internal EVA processes

  Apache License 2.0

  •1•0•0•0•Updated Sep 20, 2023Sep 20, 2023

• opencga

  Public
  An Open Computational Genomics Analysis platform for big data processing and analysis in genomics

  Java

  •

  Apache License 2.0

  •98•0•0•0•Updated Aug 12, 2023Aug 12, 2023

• eva-metrics

  Public
  Metrics Library for collecting and storing all kinds of metrics from projects and pipelines

  Java

  •3•0•0•0•Updated May 10, 2023May 10, 2023