Tools and Resources

This page summarises several additional resources and software applications useful for SARS surveillance.

Amplicon Primer Schemes

For amplicon sequencing, there are several protocols and commercial kits available. We try to summarise some of the common ones below.

ARTIC

V5.3.2

ARTIC primer scheme version 5.3.2 (link).

To analyse with nf-core/viralrecon, add these options to the command:

--genome 'MN908947.3' \
--primer_set artic \
--primer_set_version 5.3.2 \
--schema_ignore_params 'genomes,primer_set_version'

Or, alternatively, you can use the direct links to the FASTA/BED files:

--fasta 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V5.3.2/SARS-CoV-2.reference.fasta' \
--gff 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz' \
--primer_bed 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V5.3.2/SARS-CoV-2.scheme.bed'

V4.1

ARTIC primer scheme version 4.1 (link).

To analyse with nf-core/viralrecon, add these options to the command:

--genome 'MN908947.3' \
--primer_set artic \
--primer_set_version 4.1

Or, alternatively, you can use the direct links to the FASTA/BED files:

--fasta 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V4.1/SARS-CoV-2.reference.fasta' \
--gff 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz' \
--primer_bed 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V4.1/SARS-CoV-2.scheme.bed'

V4

ARTIC primer scheme version 4 (link).

To analyse with nf-core/viralrecon, add these options to the command:

--genome 'MN908947.3' \
--primer_set artic \
--primer_set_version 4

Or, alternatively, you can use the direct links to the FASTA/BED files:

--fasta 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V4/SARS-CoV-2.reference.fasta' \
--gff 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz' \
--primer_bed 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V4/SARS-CoV-2.scheme.bed'

V3

ARTIC primer scheme version 3 (link).

To analyse with nf-core/viralrecon, add these options to the command:

--genome 'MN908947.3' \
--primer_set artic \
--primer_set_version 3

Or, alternatively, you can use the direct links to the FASTA/BED files:

--fasta 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta' \
--gff 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz' \
--primer_bed 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.primer.bed'

V2

ARTIC primer scheme version 2 (link).

To analyse with nf-core/viralrecon, add these options to the command:

--genome 'MN908947.3' \
--primer_set artic \
--primer_set_version 2

Or, alternatively, you can use the direct links to the FASTA/BED files:

--fasta 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V2/nCoV-2019.reference.fasta' \
--gff 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz' \
--primer_bed 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V2/nCoV-2019.primer.bed'

V1

ARTIC primer scheme version 1 (link).

To analyse with nf-core/viralrecon, add these options to the command:

--genome 'MN908947.3' \
--primer_set artic \
--primer_set_version 1

Or, alternatively, you can use the direct links to the FASTA/BED files:

--fasta 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V1/nCoV-2019.reference.fasta' \
--gff 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz' \
--primer_bed 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V1/nCoV-2019.primer.bed'

Midnight

Primers for the “Midnight” protocol, also known as “1200” as it produces fragments that are ~1200bp long. This primer scheme is optimised for ONT platforms (link).

To analyse with nf-core/viralrecon, add these options to the command:

--genome 'MN908947.3' \
--primer_set artic \
--primer_set_version 1200

Or, alternatively, you can use the direct links to the FASTA/BED files:

--fasta 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/primer_schemes/artic/nCoV-2019/V1200/nCoV-2019.reference.fasta' \
--gff 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz' \
--primer_bed 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/primer_schemes/artic/nCoV-2019/V1200/nCoV-2019.bed'

NEB VarSkip

1a

NEB’s VarSkip kit, primer version 1a (link).

For analysis with nf-core/viralrecon the direct link to the FASTA and BED files can be given:

--fasta 'https://raw.githubusercontent.com/nebiolabs/VarSkip/main/schemes/NEB_VarSkip/V1a/NEB_VarSkip.reference.fasta' \
--gff 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz' \
--primer_bed 'https://raw.githubusercontent.com/nebiolabs/VarSkip/main/schemes/NEB_VarSkip/V1a/NEB_VarSkip.scheme.bed'

2a

NEB’s VarSkip kit, primer version 2a (link).

For analysis with nf-core/viralrecon the direct link to the FASTA and BED files can be given:

--fasta 'https://raw.githubusercontent.com/nebiolabs/VarSkip/main/schemes/NEB_VarSkip/V2a/NEB_VarSkip.reference.fasta' \
--gff 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz' \
--primer_bed 'https://raw.githubusercontent.com/nebiolabs/VarSkip/main/schemes/NEB_VarSkip/V2a/NEB_VarSkip.scheme.bed'

2b

NEB’s VarSkip kit, primer version 2b (link).

For analysis with nf-core/viralrecon the direct link to the FASTA and BED files can be given:

--fasta 'https://raw.githubusercontent.com/nebiolabs/VarSkip/main/schemes/NEB_VarSkip/V2b/NEB_VarSkip.reference.fasta' \
--gff 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz' \
--primer_bed 'https://raw.githubusercontent.com/nebiolabs/VarSkip/main/schemes/NEB_VarSkip/V2b/NEB_VarSkip.scheme.bed'

Long 1a

NEB’s VarSkip kit, primer version 1a, long primers (link).

For analysis with nf-core/viralrecon the direct link to the FASTA and BED files can be given:

--fasta 'https://raw.githubusercontent.com/nebiolabs/VarSkip/main/schemes/NEB_VarSkip/V1a-long/NEB_VarSkip.reference.fasta' \
--gff 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz' \
--primer_bed 'https://raw.githubusercontent.com/nebiolabs/VarSkip/main/schemes/NEB_VarSkip/V1a-long/NEB_VarSkip.scheme.bed'

Atoplex

ATOPlex kit.

For analysis with nf-core/viralrecon the direct link to the FASTA and BED files can be given:

--fasta 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz' \
--gff 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.gff.gz' \
--primer_bed 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/NC_045512.2/amplicon/nCoV-2019.atoplex.V1.bed'

Illumina COVIDseq

COVIDseq

The original COVIDseq kit uses ARTIC V3 primers.

See section above for nf-core/viralrecon options.

COVIDseq (RUO version)

The COVIDseq RUO version uses ARTIC V4 primers.

See section above for nf-core/viralrecon options.

SWIFT / xGEN

The “xGen SARS-CoV-2 Amplicon Panels”, previously called “SWIFT Normalase”, is commercialised by IDT. Unfortunately IDT does not make their BED files available publicly. If you purchase a kit from IDT, the company should provide you with the correct BED file to process your samples.

NOTE: in the future we will provide a link to a BED file with approximate coordinates, inferred bioinformatically. This can be useful if re-analysing public data.

Data Resources

• outbreak.info - interactive exploration of global SARS-CoV-2 data.
• Nextstrain SARS-CoV-2 resources - analysis and datasets curated by the Nextrain team.
• Data portals:
  • The European COVID-19 Data Platform
  • NCBI SARS-CoV-2 Resources
  • GISAID
• UK-specific resources:
  • COVID-19 Genomics UK Consortium
  • COVID–19 Genomic Surveillance built by the Wellcome Sanger Institute.

Web Tools

• Taxonium - a tool for large tree visualisation.

Other Courses

• Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data - using the Galaxy platform.
• The Power of Genomics to Understand the COVID-19 Pandemic - a general introduction to the COVID-19 pandemic.
• COVID-10 Data Analysis - ARTIC and CLIMB-BIG-DATA joint workshop with a series of lectures and tutorials available.