From 69763192cd549438726b7ced7934679b62f08f10 Mon Sep 17 00:00:00 2001 From: Hugo Tavares Date: Tue, 23 Jan 2024 13:02:28 +0000 Subject: [PATCH] add details about existing primer schemes; fix #34 --- materials/_chapters.yml | 1 + materials/appendices/tools_and_resources.md | 273 ++++++++++++++++++ materials/original/103-tools_and_resources.md | 27 -- 3 files changed, 274 insertions(+), 27 deletions(-) create mode 100644 materials/appendices/tools_and_resources.md delete mode 100644 materials/original/103-tools_and_resources.md diff --git a/materials/_chapters.yml b/materials/_chapters.yml index 7e2350d..6d5d0fe 100644 --- a/materials/_chapters.yml +++ b/materials/_chapters.yml @@ -28,3 +28,4 @@ book: - materials/appendices/file_formats.md - materials/appendices/unix_cheatsheet.md - materials/appendices/quick_r.Rmd + - materials/appendices/tools_and_resources.md diff --git a/materials/appendices/tools_and_resources.md b/materials/appendices/tools_and_resources.md new file mode 100644 index 0000000..4eaa0df --- /dev/null +++ b/materials/appendices/tools_and_resources.md @@ -0,0 +1,273 @@ +--- +pagetitle: "SARS Genomic Surveillance" +--- + +# Tools and Resources {.unnumbered} + +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 + +:::{.panel-tabset} +#### V5.3.2 + +ARTIC primer scheme version 5.3.2 ([link](https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V5.3.2)). + +To analyse with `nf-core/viralrecon`, add these options to the command: + +```bash +--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: + +```bash +--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](https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V4.1)). + +To analyse with `nf-core/viralrecon`, add these options to the command: + +```bash +--genome 'MN908947.3' \ +--primer_set artic \ +--primer_set_version 4.1 +``` + +Or, alternatively, you can use the direct links to the FASTA/BED files: + +```bash +--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](https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V4)). + +To analyse with `nf-core/viralrecon`, add these options to the command: + +```bash +--genome 'MN908947.3' \ +--primer_set artic \ +--primer_set_version 4 +``` + +Or, alternatively, you can use the direct links to the FASTA/BED files: + +```bash +--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](https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V3)). + +To analyse with `nf-core/viralrecon`, add these options to the command: + +```bash +--genome 'MN908947.3' \ +--primer_set artic \ +--primer_set_version 3 +``` + +Or, alternatively, you can use the direct links to the FASTA/BED files: + +```bash +--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](https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V2)). + +To analyse with `nf-core/viralrecon`, add these options to the command: + +```bash +--genome 'MN908947.3' \ +--primer_set artic \ +--primer_set_version 2 +``` + +Or, alternatively, you can use the direct links to the FASTA/BED files: + +```bash +--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](https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V1)). + +To analyse with `nf-core/viralrecon`, add these options to the command: + +```bash +--genome 'MN908947.3' \ +--primer_set artic \ +--primer_set_version 1 +``` + +Or, alternatively, you can use the direct links to the FASTA/BED files: + +```bash +--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](https://www.protocols.io/view/34-midnight-34-sars-cov2-genome-sequencing-protoc-14egn2q2yg5d/v1), also known as "1200" as it produces fragments that are ~1200bp long. +This primer scheme is optimised for ONT platforms ([link](https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/primer_schemes/artic/nCoV-2019/V1200/)). + +To analyse with `nf-core/viralrecon`, add these options to the command: + +```bash +--genome 'MN908947.3' \ +--primer_set artic \ +--primer_set_version 1200 +``` + +Or, alternatively, you can use the direct links to the FASTA/BED files: + +```bash +--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 + +:::{.panel-tabset} +#### 1a + +NEB's VarSkip kit, primer version 1a ([link](https://github.com/nebiolabs/VarSkip/tree/main/schemes/NEB_VarSkip/V1a)). + +For analysis with `nf-core/viralrecon` the direct link to the FASTA and BED files can be given: + +```bash +--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](https://github.com/nebiolabs/VarSkip/tree/main/schemes/NEB_VarSkip/V2a)). + +For analysis with `nf-core/viralrecon` the direct link to the FASTA and BED files can be given: + +```bash +--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](https://github.com/nebiolabs/VarSkip/tree/main/schemes/NEB_VarSkip/V2b)). + +For analysis with `nf-core/viralrecon` the direct link to the FASTA and BED files can be given: + +```bash +--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](https://github.com/nebiolabs/VarSkip/tree/main/schemes/NEB_VarSkip/V1a-long)). + +For analysis with `nf-core/viralrecon` the direct link to the FASTA and BED files can be given: + +```bash +--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](https://en.mgi-tech.com/products/reagents_info/33/). + +For analysis with `nf-core/viralrecon` the direct link to the FASTA and BED files can be given: + +```bash +--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 + +:::{.panel-tabset} +#### COVIDseq + +The original [COVIDseq kit](https://emea.illumina.com/products/by-type/ivd-products/covidseq.html) uses **ARTIC V3 primers**. + +See section above for `nf-core/viralrecon` options. + +#### COVIDseq (RUO version) + +The [COVIDseq RUO version](https://emea.illumina.com/products/by-type/clinical-research-products/covidseq.html) uses **ARTIC V4 primers**. + +See section above for `nf-core/viralrecon` options. +::: + + +### SWIFT / xGEN + +The "[xGen SARS-CoV-2 Amplicon Panels](https://eu.idtdna.com/pages/products/next-generation-sequencing/workflow/xgen-ngs-amplicon-sequencing/predesigned-amplicon-panels/sars-cov-2-amp-panel)", 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](https://outbreak.info/) - interactive exploration of global SARS-CoV-2 data. +- [Nextstrain SARS-CoV-2 resources](https://nextstrain.org/sars-cov-2/) - analysis and datasets curated by the Nextrain team. +- Data portals: + - [The European COVID-19 Data Platform](https://www.covid19dataportal.org/) + - [NCBI SARS-CoV-2 Resources](https://www.ncbi.nlm.nih.gov/sars-cov-2/) + - [GISAID](https://www.gisaid.org/) +- UK-specific resources: + - [COVID-19 Genomics UK Consortium](https://www.cogconsortium.uk/tools-analysis/public-data-analysis-2/) + - [COVID–19 Genomic Surveillance](https://covid19.sanger.ac.uk) built by the Wellcome Sanger Institute. + + +## Web Tools + +- [Taxonium](https://cov2tree.org/) - a tool for large tree visualisation. + + +## Other Courses + +- [Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data](https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html) - using the Galaxy platform. +- [The Power of Genomics to Understand the COVID-19 Pandemic](https://www.futurelearn.com/courses/genomics-covid-19) - a general introduction to the COVID-19 pandemic. +- [COVID-10 Data Analysis](https://www.climb.ac.uk/artic-and-climb-big-data-joint-workshop/) - ARTIC and CLIMB-BIG-DATA joint workshop with a series of lectures and tutorials available. diff --git a/materials/original/103-tools_and_resources.md b/materials/original/103-tools_and_resources.md deleted file mode 100644 index b891782..0000000 --- a/materials/original/103-tools_and_resources.md +++ /dev/null @@ -1,27 +0,0 @@ ---- -pagetitle: "SARS Genomic Surveillance" ---- - -# Tools and Resources - -## Data Resources - -- [outbreak.info](https://outbreak.info/) - interactive exploration of global SARS-CoV-2 data. -- [Nextstrain SARS-CoV-2 resources](https://nextstrain.org/sars-cov-2/) - analysis and datasets curated by the Nextrain team. -- Data portals: - - [The European COVID-19 Data Platform](https://www.covid19dataportal.org/) - - [NCBI SARS-CoV-2 Resources](https://www.ncbi.nlm.nih.gov/sars-cov-2/) - - [GISAID](https://www.gisaid.org/) -- UK-specific resources: - - [COVID-19 Genomics UK Consortium](https://www.cogconsortium.uk/tools-analysis/public-data-analysis-2/) - - [COVID–19 Genomic Surveillance](https://covid19.sanger.ac.uk) built by the Wellcome Sanger Institute. - -## Web Tools - -- [Taxonium](https://cov2tree.org/) - a tool for large tree visualisation. - -## Other Courses - -- [Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data](https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html) - using the Galaxy platform. -- [The Power of Genomics to Understand the COVID-19 Pandemic](https://www.futurelearn.com/courses/genomics-covid-19) - a general introduction to the COVID-19 pandemic. -- [COVID-10 Data Analysis](https://www.climb.ac.uk/artic-and-climb-big-data-joint-workshop/) - ARTIC and CLIMB-BIG-DATA joint workshop with a series of lectures and tutorials available.