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Software#

This page lists general purpose open source software that manipulates HGVS variant descriptions. Our intention is to help the community find software that aids in the adoption of HGVS Nomenclature. The entries below are provided by the authors; the entries are not validated or endorsed by the HVNC. Software packages are listed alphabetically. See Listing Definitions for an explanation of terms. See the submission requirements and instructions for information about submitting to this list.

Name Type License Functionality Links
hgvs Python library
  • library/python
 Apache License 2.0
  • conversion
  • normalization
  • parsing
  • transcription
  • translation
  • validation
 PubMed
Documentation
pypi_rel
coveralls
Mutalyzer
  • web api
  • web user interface
 MIT License
  • backtranslation
  • extraction
  • normalization
  • transcription
  • translation
  • validation
 PubMed
Documentation
NCBI Variation Services
  • web api
 Other/unknown
  • conversion
  • normalization
  • transcription
  • translation
  • validation
 PubMed
VariantValidator
  • web api
  • web user interface
  • library/python
 Other/unknown
  • conversion
  • normalization
  • parsing
  • transcription
  • translation
  • validation
  • liftover
 PubMed
codecov

Listing Definitions#

  • Software Type: One of:

    • Library: Software component that is used by developers when building applications
    • API (e.g., REST): Software that exposes an internet-visible programming interface that is language-independent
    • Web UI: Software used with a browser window and generally intended for broader audiences

  • License: Only open access web services and open-source software with licenses approved by the Open Source Initiative will be listed. In addition, well-recognized licenses will be preferred.

  • Functionality: Software is annotated as performing one or more of the following functions:

    • backtranslation: Can the software infer possible transcript variants from observed protein consequences?
    • conversion: Does the software convert to/from HGVS and other formats (e.g., VCF, SPDI, VRS)
    • extraction: Is the software able to generate a description from a reference and observed sequence?
    • liftover: Does the software support mapping variants between aligned genomic sequences?
    • normalization: Does the software normalize variants (e.g., 3' shift) and rewrite (e.g., ins → dup)
    • parsing: Does the software parse variant descriptions into an object model usable by the client?
    • transcription: Does the software support mapping variants between genome and transcript variants?
    • translation: Does the software infer protein consequences from transcript variants?
    • validation: Does the software provide syntactic validation (i.e., the correct form) and semantic validation (i.e., the parsed structure makes sense)?

Submissions#

Requirements#

The software must:

  • Be primarily concerned with provided the functionality listed above. Software that merely accepts or emits HGVS variant descriptions as part of their operation (e.g., variant annotation) do not meet this criterion.
  • Meet the license requirements above. Commercial software, including hybrid open-source/commercial software, will not be included.
  • Have a publication in PubMed. This requirement is intended to create a bar that implies review by peers.

Instructions#

To submit a software entry:

  • Fork the hgvs-nomenclature repo
  • Create a new entry in the docs/software/ directory using an existing entry as a template
  • Build the documentation locally (see README.md) to ensure that your software entry appears as intended
  • Submit a pull request