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schemes.yml
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/
schemes.yml
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- name: artic-v3
organism: SARS-CoV-2
organism_aliases:
- nCoV-2019
aliases:
- ARTIC/V3
developers:
- name: ARTIC network
url: https://artic.network/
vendors: []
amplicon_size: 400
bed_url: https://github.com/artic-network/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.scheme.bed
bed_checksum: ""
reference_url: https://www.ebi.ac.uk/ena/browser/api/fasta/https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3
reference_checksum: ""
citation: ""
- name: artic-v4
organism: SARS-CoV-2
organism_aliases:
- nCoV-2019
aliases:
- ARTIC/V4
developers:
- name: ARTIC network
url: https://artic.network/
vendors: []
amplicon_size: 400
bed_url: https://github.com/artic-network/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V4/SARS-CoV-2.scheme.bed
bed_checksum: ""
reference_url: https://www.ebi.ac.uk/ena/browser/api/fasta/https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3
reference_checksum: ""
citation: https://community.artic.network/t/sars-cov-2-version-4-scheme-release/312
- name: artic-v4.1
organism: SARS-CoV-2
organism_aliases:
- nCoV-2019
aliases:
- ARTIC/V4.1
developers:
- name: ARTIC network
url: https://artic.network/
vendors:
- name: Integrated DNA Technologies
url: https://eu.idtdna.com/pages/products/next-generation-sequencing/workflow/xgen-ngs-amplicon-sequencing/predesigned-amplicon-panels/artic-sc2-amp-panel
amplicon_size: 400
bed_url: https://github.com/artic-network/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V4.1/SARS-CoV-2.scheme.bed
bed_checksum: ""
reference_url: https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3
reference_checksum: ""
citation: https://community.artic.network/t/sars-cov-2-v4-1-update-for-omicron-variant/342
- name: midnight
organism: SARS-CoV-2
organism_aliases:
- nCoV-2019
aliases:
- midnight-ont-v1
- MRT001.10
developers:
- name: Nikki Freed
url: https://orcid.org/0000-0003-0921-5617
- name: Olin Silander
url: https://orcid.org/0000-0003-4105-8316
vendors: []
amplicon_size: 1200
bed_url: https://zenodo.org/record/3897530/files/SARS-CoV-2_primer_sets_RBK004_nanopore_sequencing.tab?download=1
bed_checksum: ""
reference_url: https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3
reference_checksum: ""
citation: https://www.protocols.io/view/sars-cov2-genome-sequencing-protocol-1200bp-amplic-btsrnnd6?version_warning=no
- name: midnight-ont-v2
organism: SARS-CoV-2
organism_aliases:
- nCoV-2019
aliases:
- MRT001.20
developers:
- name: Nikki Freed
url: https://orcid.org/0000-0003-0921-5617
- name: Olin Silander
url: https://orcid.org/0000-0003-4105-8316
- name: Oxford Nanopore Technologies
url: https://nanoporetech.com/
vendors: []
amplicon_size: 1200
bed_url: https://github.com/epi2me-labs/wf-artic/blob/master/data/primer_schemes/SARS-CoV-2/Midnight-ONT/V3/SARS-CoV-2.scheme.bed
bed_checksum: ""
reference_url: https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3
reference_checksum: ""
citation: https://twitter.com/freed_nikki/status/1464477513107730433
- name: midnight-ont-v3
organism: SARS-CoV-2
organism_aliases:
- nCoV-2019
aliases:
- MRT001.30
developers:
- name: Oxford Nanopore Technologies
url: https://nanoporetech.com/
vendors:
- name: Oxford Nanopore Technologies
url: https://store.nanoporetech.com/midnight-rt-pcr-expansion.html
amplicon_size: 1200
bed_url: https://github.com/epi2me-labs/wf-artic/blob/master/data/primer_schemes/SARS-CoV-2/Midnight-ONT/V3/SARS-CoV-2.scheme.bed
bed_checksum: ""
reference_url: https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3
reference_checksum: ""
citation: ""
- name: midnight-idt-v4
organism: SARS-CoV-2
organism_aliases:
- nCoV-2019
aliases:
- BCCDC-PHL_1200-v4
developers:
- name: BCCDC PHL
url: http://www.bccdc.ca/our-services/service-areas/bccdc-public-health-laboratory
vendors:
- name: Integrated DNA Technologies
url: https://eu.idtdna.com/pages/products/next-generation-sequencing/workflow/xgen-ngs-amplicon-sequencing/predesigned-amplicon-panels/sars-cov-2-midnight-amp-panel
amplicon_size: 1200
bed_url: https://github.com/BCCDC-PHL/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V1200/BCCDC-PHL_1200_v4.scheme.bed
bed_checksum: ""
reference_url: https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3
reference_checksum: ""
citation: ""
- name: varskip-neb-v1a
organism: SARS-CoV-2
organism_aliases:
- nCoV-2019
aliases:
- NEB_VarSkip-V1a
developers:
- name: New England Biolabs
url: https://international.neb.com/
vendors: []
amplicon_size: 520
bed_url: https://github.com/nebiolabs/VarSkip/blob/main/schemes/NEB_VarSkip/V1a/NEB_VarSkip.scheme.bed
bed_checksum: ""
reference_url: https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3
reference_checksum: ""
citation: https://github.com/nebiolabs/VarSkip/
- name: varskip-neb-v2a
organism: SARS-CoV-2
organism_aliases:
- nCoV-2019
aliases:
- NEB_VarSkip-V2a
developers:
- name: New England Biolabs
url: https://international.neb.com/
vendors: []
amplicon_size: 520
bed_url: https://github.com/nebiolabs/VarSkip/blob/main/schemes/NEB_VarSkip/V2a/NEB_VarSkip.scheme.bed
bed_checksum: ""
reference_url: https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3
reference_checksum: ""
citation: https://github.com/nebiolabs/VarSkip/
- name: varskip-neb-v2b
organism: SARS-CoV-2
organism_aliases:
- nCoV-2019
aliases:
- NEB_VarSkip-V2b
developers:
- name: New England Biolabs
url: https://international.neb.com/
vendors:
- name: New England Biolabs
url: https://international.neb.com/products/e7626-nebnext-artic-sars-cov-2-rt-pcr-module#Product%20Information
amplicon_size: 520
bed_url: https://github.com/nebiolabs/VarSkip/blob/main/schemes/NEB_VarSkip/V2b/NEB_VarSkip.scheme.bed
bed_checksum: ""
reference_url: https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3
reference_checksum: ""
citation: https://github.com/nebiolabs/VarSkip/
- name: varskip-neb-v1a-long
organism: SARS-CoV-2
organism_aliases:
- nCoV-2019
aliases:
- NEB_VarSkip-V1a-long
developers:
- name: New England Biolabs
url: https://international.neb.com/
vendors: []
amplicon_size: 1400
bed_url: https://github.com/nebiolabs/VarSkip/blob/main/schemes/NEB_VarSkip/V1a-long/NEB_VarSkip.scheme.bed
bed_checksum: ""
reference_url: https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3
reference_checksum: ""
citation: https://github.com/nebiolabs/VarSkip/
- name: eden
organism: SARS-CoV-2
organism_aliases:
- nCoV-2019
aliases:
- Eden/V1
developers:
- name: John-Sebastian Eden
url: https://orcid.org/0000-0003-1374-3551
- name: Eby Sim
url: https://orcid.org/0000-0002-3716-7344
vendors: []
amplicon_size: 2500
bed_url: https://github.com/Psy-Fer/SARS-CoV-2_GTG/blob/master/protocols/Eden/schemes/nCoV-2019/V1/nCoV-2019.scheme.bed
bed_checksum: ""
reference_url: https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3
reference_checksum: ""
citation: https://www.protocols.io/view/sars-cov-2-genome-sequencing-using-long-pooled-amp-kxygxeob4v8j/v1