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index.yml
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schema_version: 1.0.0-alpha
metadata: The manifest of PHA4GE tiled amplicon PCR primer scheme definitions
repository: https://github.com/pha4ge/primer-schemes
license: CC-BY-4.0
organisms:
- organism: sars-cov-2
display_name: SARS-CoV-2
aliases:
- nCoV-2019
- organism: mpxv
display_name: MPXV
aliases:
- Monkeypox virus
- organism: niv
display_name: NiV
aliases:
- Nipah virus
schemes:
- organism: mpxv
name: rigshospitalet
aliases:
- erasmus
amplicon_size: 2500
version: v1.0.0
developers:
- Martin Schou Pedersen
- Matthijs Welkers
- Marcel Jonges
- Anton van den Ouden
definition_url: https://github.com/pha4ge/primer-schemes/tree/main/schemes/mpxv/rigshospitalet/2500/v1.0.0
citations:
- https://www.protocols.io/view/monkeypox-virus-whole-genome-sequencing-using-comb-n2bvj6155lk5
license: CC-BY-SA-4.0
primer_checksum: primaschema:9acd3f5ce5711ed2
reference_checksum: primaschema:17cbcde0cfff7158
- organism: mpxv
name: yale
amplicon_size: 2000
version: v1.0.0
developers:
- Nicholas F.G. Chen
- Luc Gagne
- Matthew Doucette
- Sandra Smole
- Erika Buzby
- Joshua Hall
- Stephanie Ash
- Rachel Harrington
- Seana Cofsky
- Selina Clancy
- Curtis J Kapsak
- Joel Sevinsky
- Kevin Libuit
- Mallery I Breban
- Chrispin Chaguza
- Nathan D. Grubaugh
- Daniel J. Park
- Glen R. Gallagher
- Chantal B.F. Vogels
vendors:
- organisation_name: IDT
kit_name: Yale hMPXV Amplicon Panel
definition_url: https://github.com/pha4ge/primer-schemes/tree/main/mpxv/yale/v4
source_url: https://www.protocols.io/view/monkeypox-virus-multiplexed-pcr-amplicon-sequencin-5qpvob1nbl4o/v4
citations:
- https://dx.doi.org/10.17504/protocols.io.5qpvob1nbl4o/v4
primer_checksum: primaschema:5a221a7da2cd3a8e
reference_checksum: primaschema:81a4de73f5c665a2
- organism: niv
name: nipah
amplicon_size: 400
version: v1.0.0
developers:
- ARTIC network
definition_url: https://github.com/pha4ge/primer-schemes/tree/main/niv/nipah/400/v1.0.0
source_url: https://github.com/artic-network/primer-schemes/tree/master/Nipah/V1
license: CC-BY-SA-4.0
primer_checksum: primaschema:6cc114b4202f2a28
reference_checksum: primaschema:93e763381bcf23c8
- organism: sars-cov-2
name: artic
amplicon_size: 400
version: v1.0.0
aliases:
- ARTIC/V1
developers:
- ARTIC network
definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/artic/v1
source_url: https://github.com/quick-lab/primerschemes/tree/main/primerschemes/artic-sars-cov-2/400/v1.0.0
citations:
- https://doi.org/10.1101%2F2020.09.04.283077
license: CC-BY-SA-4.0
primer_checksum: primaschema:05eb8ddabe9d83d5
reference_checksum: primaschema:b1acd7163146bf17
status: DEPRECATED
- organism: sars-cov-2
name: artic
amplicon_size: 400
version: v2.0.0
derived_from: sars-cov-2/artic/400/v1.0.0
aliases:
- ARTIC/V2
developers:
- ARTIC network
definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/artic/v2
source_url: https://github.com/quick-lab/primerschemes/tree/main/primerschemes/artic-sars-cov-2/400/v2.0.0
citations:
- https://doi.org/10.1101%2F2020.09.04.283077
license: CC-BY-SA-4.0
primer_checksum: primaschema:70dc5635f73384fb
reference_checksum: primaschema:b1acd7163146bf17
status: DEPRECATED
- organism: sars-cov-2
name: artic
amplicon_size: 400
version: v3.0.0
derived_from: sars-cov-2/artic/400/v2.0.0
aliases:
- ARTIC/V4.0
developers:
- ARTIC network
vendors:
- organisation_name: IDT
kit_name: '10011442'
- organisation_name: Eurofins
home_page: https://eurofinsgenomics.com
definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/artic/v3
source_url: https://github.com/quick-lab/primerschemes/tree/main/primerschemes/artic-sars-cov-2/400/v3.0.0
citations:
- https://doi.org/10.1101%2F2020.09.04.283077
license: CC-BY-SA-4.0
primer_checksum: primaschema:9da9db30cf27cd53
reference_checksum: primaschema:b1acd7163146bf17
status: DEPRECATED
- organism: sars-cov-2
name: artic
amplicon_size: 400
version: v4.0.0
derived_from: sars-cov-2/artic/400/v3.0.0
aliases:
- ARTIC/V4.0
developers:
- ARTIC network
vendors:
- organisation_name: IDT
kit_name: '10011442'
- organisation_name: Eurofins
home_page: https://eurofinsgenomics.com
definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/artic/v4
source_url: https://github.com/quick-lab/primerschemes/tree/main/primerschemes/artic-sars-cov-2/400/v4.0.0
citations:
- https://doi.org/10.1101%2F2020.09.04.283077
license: CC-BY-SA-4.0
primer_checksum: primaschema:d5a3ff14f651c8c1
reference_checksum: primaschema:b1acd7163146bf17
- organism: sars-cov-2
name: artic
amplicon_size: 400
version: v4.1.0
derived_from: sars-cov-2/artic/400/v4.0.0
aliases:
- ARTIC/V4.1
developers:
- ARTIC network
vendors:
- organisation_name: IDT
kit_name: '10011442'
- organisation_name: Eurofins
home_page: https://eurofinsgenomics.com
definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/artic/v4.1
source_url: https://github.com/quick-lab/primerschemes/tree/main/primerschemes/artic-sars-cov-2/400/v4.1.0
citations:
- https://doi.org/10.1101%2F2020.09.04.283077
license: CC-BY-SA-4.0
primer_checksum: primaschema:3ef3e7bb23008684
reference_checksum: primaschema:b1acd7163146bf17
- organism: sars-cov-2
name: artic
amplicon_size: 400
version: v5.0.0
derived_from: sars-cov-2/artic/400/v4.1.0
aliases:
- ARTIC/V5
developers:
- ARTIC network
definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/artic/v5
source_url: https://github.com/quick-lab/primerschemes/tree/main/primerschemes/artic-sars-cov-2/400/v5.0.0
citations:
- https://doi.org/10.1101%2F2020.09.04.283077
license: CC-BY-SA-4.0
primer_checksum: primaschema:bdaeb59a7ef0ec12
reference_checksum: primaschema:b1acd7163146bf17
- organism: sars-cov-2
name: artic
amplicon_size: 400
version: v5.2.0
derived_from: sars-cov-2/artic/400/v5.1.0
aliases:
- ARTIC/V5
developers:
- ARTIC network
definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/artic/v5.2
source_url: https://github.com/quick-lab/primerschemes/tree/main/primerschemes/artic-sars-cov-2/400/v5.2.0
citations:
- https://doi.org/10.1101%2F2020.09.04.283077
license: CC-BY-SA-4.0
primer_checksum: primaschema:d57ec2cdb00e2583
reference_checksum: primaschema:b1acd7163146bf17
- organism: sars-cov-2
name: artic
amplicon_size: 400
version: v5.3.2
derived_from: sars-cov-2/artic/400/v5.2.0
aliases:
- ARTIC/V5.3.2
developers:
- ARTIC network
definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/artic/v5.3.2
source_url: https://github.com/quick-lab/primerschemes/tree/main/primerschemes/artic-sars-cov-2/400/v5.3.2
citations:
- https://doi.org/10.1101%2F2020.09.04.283077
license: CC-BY-SA-4.0
primer_checksum: primaschema:5c6856dfe0e2537d
reference_checksum: primaschema:b1acd7163146bf17
- organism: sars-cov-2
name: artic
amplicon_size: 400
version: v5.4.2
derived_from: sars-cov-2/artic/400/v5.3.2
aliases:
- ARTIC/V5.4.2
developers:
- ARTIC network
definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/artic/v5.4.2
source_url: https://github.com/quick-lab/primerschemes/tree/main/primerschemes/artic-sars-cov-2/400/v5.4.2
citations:
- https://doi.org/10.1101%2F2020.09.04.283077
license: CC-BY-SA-4.0
primer_checksum: primaschema:294136d77eb67db8
reference_checksum: primaschema:b1acd7163146bf17
- organism: sars-cov-2
name: eden
amplicon_size: 2500
version: v1.0.0
aliases:
- sydney
developers:
- John-Sebastian Eden
- Eby Sim
definition_url: https://github.com/pha4ge/primer-schemes/blob/main/schemes/sars-cov-2/eden/2500/v1.0.0
citations:
- https://dx.doi.org/10.17504/protocols.io.befyjbpw
notes:
- Protocol includes addendum for ONT sequencing
license: CC-BY-4.0
primer_checksum: primaschema:55c9726eb1400cab
reference_checksum: primaschema:b1acd7163146bf17
- organism: sars-cov-2
name: midnight
amplicon_size: 1200
version: bccdc-v1.0.0
derived_from: midnight-v1
developers:
- Nikki Freed
- Olin Silander
- John Tyson
- Tracy Lee
citations:
- https://dx.doi.org/10.17504/protocols.io.bwyppfvn
notes:
- Accomodates P.1
license: CC-BY-4.0
status: DEPRECATED
primer_checksum: primaschema:63730c2cad698b52
reference_checksum: primaschema:b1acd7163146bf17
- organism: sars-cov-2
name: midnight
amplicon_size: 1200
version: bccdc-v2.0.0
derived_from: bccdc-v1.0.0
developers:
- Nikki Freed
- Olin Silander
- John Tyson
- Tracy Lee
citations:
- https://dx.doi.org/10.17504/protocols.io.bwyppfvn
notes:
- Accomodates BA.1
license: CC-BY-4.0
status: DEPRECATED
primer_checksum: primaschema:24946c8acfd9e9df
reference_checksum: primaschema:b1acd7163146bf17
- organism: sars-cov-2
name: midnight
amplicon_size: 1200
version: bccdc-v3.0.0
derived_from: bccdc-v2.0.0
developers:
- Nikki Freed
- Olin Silander
- John Tyson
- Tracy Lee
citations:
- https://dx.doi.org/10.17504/protocols.io.bwyppfvn
license: CC-BY-4.0
status: DEPRECATED
primer_checksum: primaschema:76400a085952e90c
reference_checksum: primaschema:b1acd7163146bf17
- organism: sars-cov-2
name: midnight
amplicon_size: 1200
version: bccdc-v4.0.0
aliases:
- midnight-idt-v2
derived_from: bccdc-v3.0.0
developers:
- Nikki Freed
- Olin Silander
- John Tyson
- Tracy Lee
citations:
- https://dx.doi.org/10.17504/protocols.io.bwyppfvn
notes:
- Accomodates Omicron BA.2
- IDT calls this the "-Midnight-1200 Amplicon Panel" and "Midnight Amplicon Panel
v2"
definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/midnight/bccdc-v4
license: CC-BY-4.0
status: DEPRECATED
primer_checksum: primaschema:fbdd06cb1617a6f9
reference_checksum: primaschema:b1acd7163146bf17
- organism: sars-cov-2
name: midnight
amplicon_size: 1200
version: ont-v3.0.0
aliases:
- Midnight-ONT/V3
derived_from: sars-cov-2/midnight/1200/v2
developers:
- Nikki Freed
- Olin Silander
- Oxford Nanopore Technologies
vendors:
- organisation_name: Oxford Nanopore Technologies
kit_name: MRT001.30
definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/midnight/v3
citations:
- https://dx.doi.org/10.17504/protocols.io.bwyppfvn
notes:
- Accomodates Omicron BA.2
license: CC-BY-4.0
primer_checksum: primaschema:1969577706571a6e
reference_checksum: primaschema:b1acd7163146bf17
- organism: sars-cov-2
name: midnight
amplicon_size: 1200
version: v1.0.0
aliases:
- midnight-ont-v1
- Midnight-ONT/V1
- V1200
developers:
- Nikki Freed
- Olin Silander
vendors:
- organisation_name: Oxford Nanopore Technologies
kit_name: MRT001.10
- organisation_name: Integrated DNA Technologies
definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/midnight/v1
citations:
- https://dx.doi.org/10.17504/protocols.io.bwyppfvn
license: CC-BY-4.0
status: DEPRECATED
primer_checksum: primaschema:5f4389079f1acc9c
reference_checksum: primaschema:b1acd7163146bf17
- organism: sars-cov-2
name: midnight
amplicon_size: 1200
version: v2.0.0
aliases:
- midnight-ont-v2
- midnight-idt-v1
- Midnight-ONT/V2
derived_from: midnight-v1
developers:
- Nikki Freed
- Olin Silander
vendors:
- organisation_name: Oxford Nanopore Technologies
kit_name: MRT001.20
definition_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/midnight/v2
citations:
- https://dx.doi.org/10.17504/protocols.io.bwyppfvn
notes:
- Accomodates Omicron BA.1 with single primer addition
- https://twitter.com/freed_nikki/status/1464477522448433156
- Not considered a new version by Freed et al. and IDT despite additional primer
license: CC-BY-4.0
status: DEPRECATED
primer_checksum: primaschema:eafcbe457b8a2345
reference_checksum: primaschema:b1acd7163146bf17