add details about existing primer schemes; fix #34

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

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.