Skip to main content

Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses

Project description

variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.

varVAMP

language License: GPL v3 PiPy PiPy CONDA CONDA DOI

For a lot of virus genera it is difficult to design pan-specific primers. varVAMP solves this by introducing ambiguous characters into primers and minimizes mismatches at the 3' end. Primers might not work for some sequences of your input alignment but should recognize the large majority.

varVAMP comes in three different flavors:

varVAMP logo

SINGLE: varVAMP searches for the very best primers and reports back non-overlapping amplicons which can be used for PCR-based screening approaches.

single

TILED: varVAMP uses a graph based approach to design overlapping amplicons that tile the entire viral genome. This designs amplicons that are suitable for Oxford Nanopore or Illumina based full-genome sequencing.

tiled

QPCR: varVAMP searches for small amplicons with an optimized internal probe (TaqMan). It minimizes temperature differences between the primers and checks for amplicon secondary structures.

qpcr

Documentation

Already established primer schemes

We, in collaboration with specialists for the respective viruses, have already designed and wet-lab evaluated primer schemes for various viral pathogens. All the input data and varVAMP outputs are freely available here.

If you design primers for a particular pathogen, we will be happy to include them in this repo and make it freely available. Just contribute via an issue or pull request!

Citing varVAMP (coming soon)

Please cite with the respective DOI of the version you used:

varVAMP: automated pan-specific primer design for tiled full genome sequencing and qPCR of highly diverse viral pathogens.

(paper currently under preparation)


Important disclaimer: For the primer design, varVAMP uses primer3 to check if digested kmers of a sequence are potential primers. Some of the functions for this were adapted from primalscheme and I do not claim credit.

The remaing code is under the GPLv3 licence. The code is WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

varvamp-1.1.2.tar.gz (38.8 kB view details)

Uploaded Source

Built Distribution

varvamp-1.1.2-py3-none-any.whl (42.9 kB view details)

Uploaded Python 3

File details

Details for the file varvamp-1.1.2.tar.gz.

File metadata

  • Download URL: varvamp-1.1.2.tar.gz
  • Upload date:
  • Size: 38.8 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/5.0.0 CPython/3.12.2

File hashes

Hashes for varvamp-1.1.2.tar.gz
Algorithm Hash digest
SHA256 391281c3f00436f88a63b659afbac5e32a215964e4ee9c0f82cbd0dcc4dcefec
MD5 4d3b1967458468518e1b8d4552b56d3c
BLAKE2b-256 9de1e1a685228b73f1cc254c66051e866a80d93b02638556135639d057a58388

See more details on using hashes here.

File details

Details for the file varvamp-1.1.2-py3-none-any.whl.

File metadata

  • Download URL: varvamp-1.1.2-py3-none-any.whl
  • Upload date:
  • Size: 42.9 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/5.0.0 CPython/3.12.2

File hashes

Hashes for varvamp-1.1.2-py3-none-any.whl
Algorithm Hash digest
SHA256 f9a162c6ca6c36334d0ae3e8e1e76d09635e393a3170e50b14e6687634eb6a8e
MD5 4b897787d82ec1557907d13bccacfdd0
BLAKE2b-256 3b54d8035c7afe8896138704d2ee5cacc9a57b53d89e9b76898d4ea8c3ef5818

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page