Merge branch 'add_virus_configs'

- Virus definitions
- More documentation to address V-pipe 3.0 review

.github/workflows/README.md

@@ -0,0 +1,3 @@
+This directory stores workflow scripts that are picked up by GitHub Actions to automatically perform test installations of V-pipe on Mac OS and Linux systems and run end-to-end tests by executing tutorials with real example data.
+This ensures successful installation and reproducible execution on different systems.
+For each update of V-pipe these workflow scripts are automatically executed and report about installation problems or troubles on the test data

README.md

@@ -33,6 +33,11 @@ Also see [snakemake's documentation](https://snakemake.readthedocs.io/en/stable/
 
 Tutorials introducing usage of V-pipe are available in the [docs/](docs/README.md) subdirectory.
 
+
+### Tutorials
+
+Tutorials for your first steps with V-pipe for different scenarios are  available in the [docs/](docs/README.md) subdirectory.
+
 ### Using quick install script
 
 To deploy V-pipe, use the [installation script](utils/README.md#quick-installer) with the following parameters:
@@ -50,6 +55,8 @@ cd work
 ./vpipe --jobs 4 --printshellcmds --dry-run
 ```
 
+Test data to test your installation is available with the tutorials provided in the [docs/](docs/README.md) subdirectory.
+
 ### Using Docker
 
 Note: the [docker image](https://github.com/cbg-ethz/V-pipe/pkgs/container/v-pipe) is only setup with components to run the workflow for HIV and SARS-CoV-2 virus base configurations.

config/drosophila_c_virus.yaml

@@ -0,0 +1,32 @@
+# config-file used for the analysis of drosphila C virus Illumina samples
+# Lezcano et al., Virus Evolution, 2023, https://doi.org/10.1093/ve/vead074
+# NCBI BioProject accession number PRJNA993483
+
+general:
+      aligner: "bwa"
+      snv_caller: "shorah"
+
+input:
+    reference: resources/drosphila_c_virus/NC_001834.1.fasta
+    datadir: resources/samples/
+    read_length: 100
+    samples_file: samples.tsv
+    paired: true
+
+consensus_bcftools:
+    max_coverage: 150000
+
+snv:
+  consensus: false
+  disk_mb: 1250
+  mem_mb: 35000
+  time_min: 6000
+  threads: 64
+
+output:
+    snv: true
+    local: true
+    global: false
+    visualization: false
+    diversity: false
+    QA: false

config/h3n2_ha.yaml

@@ -0,0 +1,75 @@
+# config-file used for the analysis of H3N2 segment HA
+# config file was used to analysis wastewater Illumina data from SRA available
+# through the SRA Run accession: SRP385331
+
+general:
+    aligner: bwa
+    primers_trimmer: samtools
+    threads: 6
+    snv_caller: lofreq
+    temp_prefix: ./temp
+    preprocessor: skip
+
+input:
+    datadir: samples/
+    samples_file: samples.tsv
+    reference: "{VPIPE_BASEDIR}/../resources/h3n2_ha/h3n2_ha.fasta"
+    genes_gff: "{VPIPE_BASEDIR}/../resources/h3n2_ha/gffs/h3n2_ha.gff3"
+    paired: true
+    read_length: 151
+
+output:
+    datadir: results/
+    snv: True
+    local: True
+    global: False
+    visualization: False
+    QA: False
+    diversity: False
+
+gunzip:
+    mem: 100000
+
+extract:
+    mem: 100000
+
+preprocessing:
+    mem: 10000
+
+sam2bam:
+    mem: 5000
+
+ref_bwa_index:
+    mem: 65536
+
+bwa_align:
+    mem: 40690
+    threads: 8
+
+bowtie_align:
+    mem: 12288
+    threads: 6
+
+coverage:
+    mem: 131072
+    threads: 32
+    time: 60
+
+minor_variants:
+    mem: 16384
+    threads: 64
+
+coverage_intervals:
+    coverage: 0
+    mem: 2000
+    threads: 1
+
+lofreq:
+    consensus: false
+
+snv:
+    consensus: false
+    localscratch: $TMPDIR
+    time: 240
+    mem: 1024
+    threads: 64

config/herpes_simplex_virus_2.yaml

@@ -0,0 +1,34 @@
+# config-file used for the analysis of herpes_simplex_virus_2 Illumina samples
+# Lezcano et al., Virus Evolution, 2023, https://doi.org/10.1093/ve/vead074
+# deletion analysis
+# analysed sample is from  López-Muñoz AD, Rastrojo A, Kropp KA, Viejo-Borbolla A, Alcamí A. Combination of long- and short-read sequencing fully resolves complex repeats of herpes simplex virus 2 strain MS complete genome. Microb Genom. 2021 Jun;7(6).
+# Sample accession number: ERR3278849
+
+general:
+      aligner: "bwa"
+      snv_caller: "shorah"
+
+input:
+    reference: resources/herpes_simplex_virus_2/MK855052.1.fasta
+    datadir: resources/samples/
+    read_length: 250
+    samples_file: samples.tsv
+    paired: true
+
+consensus_bcftools:
+    max_coverage: 150000
+
+snv:
+  consensus: false
+  disk_mb: 1250
+  mem_mb: 35000
+  time_min: 6000
+  threads: 64
+
+output:
+    snv: true
+    local: true
+    global: false
+    visualization: false
+    diversity: false
+    QA: false

config/polio.yaml

@@ -0,0 +1,25 @@
+# config-file used for the analysis of poliovirus MinION samples
+# sample accession number: ERR4027774 (Shaw et al., 2020, DOI: https://doi.org/10.1128/jcm.00920-20)
+
+general:
+    virus_base_config: ""
+    aligner: minimap
+    preprocessor: skip
+
+input:
+    reference: resources/polio/AY560657.1.fasta
+    datadir: resources/samples/
+    samples_file: config/samples.tsv
+    paired: false
+
+output:
+    trim_primers: false
+    snv: false
+    local: false
+    global: false
+    visualization: false
+    QA: false
+    diversity: false
+
+minimap_align:
+    preset: map-ont

config/rsvb.yaml

@@ -0,0 +1,27 @@
+# config file for Human respiratory syncytial virus B
+# config file is used to process Illumina RSV samples
+
+general:
+    virus_base_config: ""
+    preprocessor: "prinseq"
+    aligner: "bwa"
+    primers_trimmer: "samtools"
+
+input:
+    datadir: "samples/"
+    samples_file: "samples.tsv"
+    read_length: 251
+    primers_bedfile: "{VPIPE_BASEDIR}/../resources/rsvb/RSVB_primers_400_V2.1.bed"
+    inserts_bedfile: "{VPIPE_BASEDIR}/../resources/rsvb/RSVB_inserts_400_V2.1.bed"
+    reference: "{VPIPE_BASEDIR}/../resources/rsvb/MT107528.1.fasta"
+
+output:
+    datadir: "results"
+    trim_primers: true
+    snv: false
+    local: false
+    global: false
+snv:
+    consensus: false
+lofreq:
+    consensus: false

resources/auxiliary_workflows/benchmark/resources/multi_setup/README.md

@@ -0,0 +1,20 @@
+This repository contains the Snakemake workflow to reproduce the benchmarking study for the global haplotype reconstruction methods presented in https://doi.org/10.1101/2023.10.16.562462.
+
+The notebooks in the directory `workflow/notebooks/` can be used to reproduce the figures of Figure 4.
+
+Here is a step-by-step guide on how to run this workflow.
+1. Clone the repository of V-pipe 3.0 into your working directory: `git clone https://github.com/cbg-ethz/V-pipe.git`  
+2. Go into the directory of the benchmarking study for the global haplotype reconstruction `cd V-pipe/resources/auxiliary_workflows/benchmark/resources/multi_setup`  
+3. The parameters to reproduce the synthetic dataset of varying coverage is here: `config_varycoverage/params.csv` with the configuration file `config_varycoverage/config.yaml` where simulation mode, replicate number and methods to be executed are defined.  
+4. The parameters to reproduce the synthetic dataset of varying distance pattern is here: `config_varyparams/params.csv` with the configuration file `config_varyparams/config.yaml` where simulation mode, replicate number and methods to be executed are defined.  
+5. The parameters to reproduce the real dataset is here: `config_realdata/params.csv` with the configuration file `config_realdata/config.yaml` where replicate number and methods to be executed are defined.  
+6. The methods to execute must be define in a Python script in this directory: `V-pipe/resources/auxiliary_workflows/benchmark/resources/method_definitions`
+- Haploclique: `V-pipe/resources/auxiliary_workflows/benchmark/resources/method_definitions/haploclique.py`  
+- PredictHaplo: `V-pipe/resources/auxiliary_workflows/benchmark/resources/method_definitions/predicthaplo.py`  
+- HaploConduct: `V-pipe/resources/auxiliary_workflows/benchmark/resources/method_definitions/haploconduct.py`  
+- CliqueSNV: `V-pipe/resources/auxiliary_workflows/benchmark/resources/method_definitions/cliquesnv.py`
+7. Now the workflow is ready, go back to the directory `V-pipe/resources/auxiliary_workflows/benchmark/resources/multi_setup`.   
+8. To install the needed Conda environments execute: `snakemake --conda-create-envs-only --use-conda -c1`.   
+9. To submit the workflow to a lsf-cluster execute `./run_workflow.sh`, otherwise execute the workflow with `snakemake --use-conda -c1`
+10. The workflow will provide the results in the directory `results`.
+11. When the workflow has terminated and all result files were generated, figures from Figure 4 from the manuscript can be generated by executing the notebooks in  `workflow/notebooks/`.  

resources/drosophila_c_virus/NC_001834.1.fasta

@@ -0,0 +1,134 @@
+>NC_001834.1 Drosophila C virus strain EB, complete genome
+TTTATATCGTGTGTACATATAAATATGTACACACGGCTTTTAGGTAGAATATTGTTTTCAATGTTGATTT
+TAAAGGTAACTTTGGTTATTATGCTTTACGGTTTTCATTGTTGATGGTATTTGTGGCCTGCGGTCCCTAA
+TTGTTGAATTATTTATTCTGATACGTTGTTTTCATTGTTGATGGTAAGGATTCTTATTTTGAAGTGGTTT
+TTCAGAAGATAACTCTAAATATGAATTATGCCTTATTGTTTTCAATGTTGATGGCCTTCGTTTAAATACT
+CTTTGTTAATGACGGTAATCAAAGATTACATCTCAAACTTAGATTAATATTTTTAAGTAGGGTATACTGA
+GTTAGTCCTCTCTCTTTACTGATTTTGATATCTGGTAATTGACTTCGAAGAAAGATGCGTCTTTTGGATT
+TGTAATGACTGGGCCTTAAGTTCATAGGTGTTATTACATGGAGGAACACATTACTTTGGTTGATGATGAT
+GTTTTGATGATGACTTTCAATGTATGTGCTTATGTTAAGCCTGACATAAGAACTTACTAGTTTGCATAAT
+GCAAAGGGTTAGTATATGATTTTTAGTATGTGGATTTTGACACTGCCTTTGATTAGGATGTGTGAATGAT
+TTTGAAACATATTAAGATGTTTATACGAGCGTGTTGTTTACTATTTTCAGGATATGTGGAAGCGGTTGTG
+TATGATCTATACGCACATTTAGTTCCCAGAGGGCGTTGTCGTCTCCCCCTAAGCAAGGGAGAAACACGTG
+GCACATGATCTTGCGCTTAACGATAAAAATGGAATCTGATAAAAGTATGGCCTGTTTAAATAGAATTTTG
+ATGAATAAGATGATGTTTGTGGAAGATAAGATCTCTACCCTTAAGATGGTTGCTGATTATTATCAAAAAG
+AAGTAAAGTATGATTTTGATGCAGTTGAATCTCCCCGTGAGGCACCTGTATTTAGATGTACTTGTCGATT
+CCTTGGTTATACCATTATGACTCAAGGCATCGGTAAGAAGAATCCGAAACAGGAAGCTGCACGTCAGATG
+TTGCTCTTGTTATCAGGAGATGTTGAGACTAACCCTGGACCCGTTCAATCGCGCCCCGTGTATTATCGTT
+ACAACGACCCTAGATATACACGGTTGGAAAAAGCTATTGAACGTCGAGACGATAAAATTAAAACATTAAT
+TAAAGAGTTGCGTCGACAAATCAAAAATAGGAAAATTTATTCCCAAGGAATGTTTGATAAATTAACTAAA
+CAAATTTCTGATGGGATAAAAGATGGTGTTGGCTCTGAACAGATGAATGGAAATTTGACTCGTATTTGTG
+ATTTCCTAGAGAACACTCTTCCTGGGTTACAAGCAAATATTCAAGCCACTGTGATTGATACAACAGACAA
+ATATGTTTCTTTAAAAGAGGATATTATGAAGATTGTTTTAGTGATATTGCTTGTTCGTCTTTTAATGGTT
+TGGAAGAAGTATCGTGCTTCTCTGTGTGTTATTTTAATCTTTATTTTTAAATTTTATGGATTCGATCAAA
+AGTTGATTGATTTAATTATGGATTTGAAGAATAAAATATTTTCACAGGGTGCATTGGAAGATACAGTTGA
+GGAGGTTGTATATCATCCTTGGTTCCATACGTGTGGAAAAATCATCTTTGCGGTTATGGCTTTCTTAACA
+ATTAAGAAAATTCCTGGTAAACAGGATTGGGATAGTTACATAACACGTTTAGATCGTATCCCAAAATCTA
+TTGAGGGAGCTAAAAAGATCACTGATTACTGTTCAGAATATTTTAATATTGCTAATGATCAGATCAAGAT
+GATGGTTCTTGGAAAGACTAAAGAAGAATTGCAACGTGCTAATGGACTATATGGAGAAATTCAAGCTTGG
+GCTCAAGAGGTTCGCCAGTATTTGGAATTGGATCAACGGAATAAAATTGATCTAGATACTGAAACCGCAA
+ATCGTGTTGAACAACTTTGGATAAAGGGCTTGAAATTCAAGAGTGAACCCCTTTTGAGTAAGGAAATGTC
+AGCTTTAGTTCATACAACTCTTTTACCAGCTAAGCAATTGTACGAGTATGTATCGTGTTCTCCTGTTAAA
+GGGGGAGGACCACGTATGCGTCCAATTTGTTTATGGTTGGTAGGTGAATCAGGAGTTGGTAAGACTGAAA
+TGGTATATCCATTGTGCATTGATGTTCTTCGGGAAATGGGGATGATTAAGAAAGATGATTTTCATCATCA
+AGTTTATGGTCGTCAAGTTGAAACTGAATTCTGGGATGGTTATAAAGGACAGAAAATTGTCATTTATGAT
+GATGCATTTCAGAAGAAAGATGACAAAACAGCAGCTAACCCAGAAATTTTTGAGGTTATTCGCTCTTGCA
+ACACTTTTCCTCAGCATTTACATATGGCAGCTCTTCATGATAAAAATACTTTTTCTGCTGCTGAATTACT
+CTTATATACCACTAATGATTATAATGTTAAGCTGGAATCTATTACTTTTCCCGATGCTTTCTTTAATCGT
+ATGGGCGATATGGCTTATAAAGTTAGTCCTAAGAAAGAGTATGGTATTGAAACCGAGAAAGGGAATTCAG
+GTAAAACTTATTTAAAATTGGATAAGAGTAAATTGGACAAAACAAAAGCTATTGACCTTTCAGTGTATGA
+ATTCCAAAAAATTGTACGTGACGAGAAAAGTGATGCAGGTTGGATTGATTCTGGATCACCCTTGGACTAT
+GAAGATTTTGCTAAATTAGTGTGTTCAAAATGGAAAGAAGCGAAACAATCTTCAATGAATAAATTGAAAT
+TTTTGGAAGAATATGCTATTCGTGCTCAGGTTGGATCAGAAGAAAATTCTGAATATGGTGATTGTATAGA
+TTTTGTCGATGATATTGCCAAACGCTTACAAAAAGGTGAAACTCTTGAAGAAATAGAGTTTGATTATGCC
+TCAGATCCAGAGATGTTTACTCAATACTATCATTTTAAATCTACAATTAAACCGGCATCGCGTTGGCAGA
+AGTATAAGGATCGGATGGACATTTGTTTGAGCGACTGTAAGACTTATTTAGCAAAGAAATACGAAGAAAT
+TAAGAAAATTCTTGCCGAACATCCTATCTTGACGATTTTAGGAATGATAGGGGTTGCCTTATCTGCTCTG
+GCAATGTACTATTGGTTTTCTAAATCGTTGGATCCTGTAGAAGCCGAGGTTGCTCCTTCTGGTGACGCTA
+AAACAGTGCGCTTACCAAGGAAACTCGTTGAGATTGGTGCTTCTGGAGATGTTAAAACACAGAAGATTGT
+GAAACCCGTTGTAGAGACCGAATGGCATCGTAACAATAAAGGAGAGATTGAAATTTCTTGTGATGAATGT
+GGTATGCATAGGATGTCTGCATTTAACAATATGACAGATGAAGAATTTGATAACTGTACATATGAAGATT
+TGAATAAGGACCAGAAACGTGAACTTGCCCAGTGGTCTACTAAAGATTCTTGGTTAGGTCGATTCTTTTT
+GAGTCGAGATCGCAAGAATAAGGTTGGAATTTGGGCCGAAGTGGGACAATCAGGTGATGTTAAAACAAAT
+AAAGCTCAGATTAAACGTGTTGAAGCTGGAGCCGAAGAATTAGTTACTGTTGCTTTAACTCAAGGTTGTT
+CTGATGATGCTGCACACAATTTGATGATTGACGTTTTCCAAAAAAATACATATAGAATGTCATACTTCCG
+TGGAGACAAGCGTTATCAACTTGGAAATTGTACATTTGTTCGTGGTTGGTCTTTTATTATGCCATATCAT
+TTTGTACAGGCTGTGTTTGCGCGAAGATTGCCACCTAACACGATTATTTCTTTGTCCCAACAGATGTCTG
+AAGATTTAATGCAAATTCCATTATCACACTTCTTTTCTGCTGGTGTTGACAATTTTTATTTAACAGATAA
+TTGTGTGCGCTTGCCATTTAAAAATGGAGATTTTCGCGATTGTGTTATGGTTAATTTACATTCACGAATG
+TGCACGCCACATCGTGATTTGGTTCGGCATTTTATTTTAACTTCTGATCAAGGTAAATTGAAGGGATCTT
+TTAGTGGTGCAATGGCAACTTTCCATGTTAACAATATGGGTTTATATCGTGTTTATAATTGGCTAAATGC
+AGTTCGTCCTTGCGATAAAAAGATAGAAATTTTCCACCCTGAAGATGGTTTTGAGTATCCCGAAGAATCA
+TATATTCAACGTGACTGTTATGAATATAATGCACCGACTCGTACTGGGGATTGTGGATCTATTATTGGAT
+TGTATAATAAATATTTAGAAAGGAAAATCATCGGTATGCACATTGCTGGAAATGATGCAGAAGAGCATGG
+TTATGCGTGCCCTTTGACACAAGAGTGTCTTGAGACTGCTTTTTCTGCTTTAGTAAATAAAAATAAGAAG
+AATATTTCCTCACAATTTTATTATGAAATACCCAATATGGTTGATCCACTCGGTGATAGTAGTGTTCCTG
+AAGGTAAGTTTTACGCTTTAGGAAAGTCATCTATTCGTGTGGGACAGGCAGTTAATTCGTCCATAATTCC
+TTCTCGAATTTATGGGAAGTTGTCTGTTCCTACAATGAAACCAGCACTACTCAAGCCAACGATTCTGAAT
+AACAAAGTACATAATCCTTTATTGTCGGGACTTAAGAAATGTGGTGTAGACACTGCGGTCTTGAGTGATG
+ATGAAGTTTTGAGTGCTTCACAAGATGTTTGTCGTGTTATGTTGAACCAATATAATAAAAATTTGAATAA
+AACAAAGTATCAACGCATTTTAACATATGAGGAAGCTATTCGTGGAACCCAAGATGATGAATTTATGTGT
+GCTATTAATCGTACAACGTCACCAGGATTTCCTTATGCACAAATGAAAAGAAATGCTCCAGGTAAACAGC
+AATGGATGGGTTTTGGTGAAGAATTTGATTTTACAAGTAATTATGCACTAGCTTTGCGGAAAGATGTTGA
+ACAACTCATTGAAGATTGTGCTAGCGGAAAAATATCTAATGTCATTTTTGTAGATACATTGAAAGATGAG
+CGACGCGATATAGCTAAAGTAAATGTAGGTAAAACGCGTGTATTTTCTGCAGGTCCTCAACATTTTGTAG
+TTGCATTTCGCCAATATTTCCTACCTTTTGCTGCTTGGTTGATGCATAATCGCATTTCGAACGAAGTAGC
+AGTTGGCACTAATGTTTATTCATCTGATTGGGAACGTATTGCAAAACGTCTTAAAACAAAAGGTAGTCAC
+GTCATTGCGGGGGACTTTGGAAATTTCGATGGATCTTTAGTAGCACAAATTTTGTGGGCCATATTTTGGG
+AAATTTTTGTTGTATGGCTTAAGCAATTTATTGATATAGAGAATTCAGAAGGAAAACGTATTTTATGTAT
+CTGTCTTGGTTTGTGGTCACATTTAGTTCACTCTGTTCATATTTATGAAGATAATGTATATATGTGGACT
+CATTCTCAACCTTCTGGCAATCCTTTCACTGTTATTATTAATTGCTTGTATAATTCGATTATTATGCGAC
+TGTCATGGATTCGTGTGATGGAGAAATTTCAACCTAGACTTAAGTCCATGAAGTGGTTCAACGAATATGT
+CGCCTTGATAACATATGGTGACGACAATGTTTTAAACATTGATGCAAAGGTTGTGGAATGGTTTAATCAG
+ATTAACATTAGTGAGGTTATGACTGAAATGCGACATGAATATACGGACGAAGCTAAAACTGGTGATATTG
+TTAAATCTCGTAAATTAGAAGATATTTTCTTTTTGAAGAGAAAATTTCGTTTTAGCCCAGAATTACAACG
+CCATGTTGCTCCATTGAAGATCGAAGTTATTTATGAAATGTTGAATTGGTCTCGCCGCTCTATAGATCCA
+GATGAAATCTTGATGTCGAACATTGAAACGGCTTTTCGTGAAGTAGTTTACCACGGAAAAGAAGAATACG
+ATAAACTAAGGTCAGCGGTATTGGCGTTGAAGGTACCCCAGGAACTTCCTGAAAACCCTCAGATTTTGAC
+GTACAACCAATATTTGCACGATATTGAATATCTTGCGGACCCTTTGTACGACTTTTAGTTAAGATGTGAT
+CTTGCTTCCTTATACAATTTTGAGAGGTTAATAAGAAGGAAGTAGTGCTATCTTAATAATTAGGTTAACT
+ATTTAGTTTTACTGTTCAGGATGCCTATTGGCAGCCCCATAATATCCAGGACACCCTCTCTGCTTCTTAT
+ATGATTAGGTTGTCATTTAGAATAAGAAAATAACCTGCTAACTTTCAAACAAATAATAATAACATTGAAA
+ATGAAGATCGGAAAATTACTTCCGAGCAAAAAGAGATTGTACACTTTTCTAGTGAAGGAGTTACCCCTAG
+TACCACTGCGGTGCCTGATATCGTTAGTCTTTCAACAGATTATTTGTCTATGACTACTCGTGAAGATCGT
+ATCCACACGATTAAAGATTTTCTTTCTCGTCCAATTATAATTCAAACTGGTCTTTGGTCTTCCGCTACAA
+CTGCCGAAACTCAATTGTATACTGCTAATTTCCCTGAAGTGTTCATTTCTAATACTATGTATCAAGAAAA
+GTTGCGTGGGTTCGTGGGTTTGCGAGCAACTTTAGTCATTAAAGTGCAAGTGAATTCCCAACCTTTCCAG
+CAAGGACGATTGATGCTACAGTATTATCCGTATGCACAGTATATGCCTAACCGTGTTTCTTTGGTGAATT
+CCACTCTCCAAGGACGCTCTGGTTGTCCTCGAACAGATTTGGATTTGAGCGTTGGTACGGAAGTTGAAAT
+GCGAATTCCTTATGTGTCCCCTCATGTATATTACAATCTTATTACTGGACAAGGATCATTTGGCGCTATA
+TATTTGGTTGTATATAGCCAACTAAGAGATCAAGTTACAGGAACAGGTTCTGTTGAATATACTGTTTGGG
+CTCATTTGGAAGATGTAGATGTGCAATACCCGACCGGTGCAAACATTTTCACGGGTAGCTCTCCAAATTT
+TGCCTCTTTGGGTCAGAAAATGAGTGATGGAAAATTCACTGAAAAAGACTTGAGAGATATTTGGACTTCA
+AAAGCGTACAATAAACAACCAGACAAAATTTTCGCACAAGTGGCTTCTGAAATAACACAACTCAAAGAAT
+CAGGAACAATTAGTTCTGGAATTGGACAAGTTTCTGAAGGTCTTTCTACCATGTCTAAAATCCCTATACT
+CGGAAATATGTTTACAAAACCCGCCTGGATTTCAGCTCAAGTATCTAATATCTTCAAGATGCTTGGTTTT
+TCAAAACCCACTGTTCAAGGTCTTCCTTGTGAATCGAAACTGCGTGGTCAAGTTCGAATGGCGAATTTTG
+ATGGCGCTGATACATCACATAAATTGGCTTTGTCTGCCCAAAACGAAATTGAAACAAAATCTGGACTTTC
+TGGAACTTCTCCTGATGAAATGGATTTATCACACGTCCTTTCCATACCAAATTTTTGGGATCGTTTTACT
+TGGAACACAACCGATGCCACTAGTTCTATTTTATGGGATAATTATGTTACACCAATGAAAATTAAACCAT
+ATTCCTCTACAATATTAGATAGATTTAGATGCACTCATATGGGTTTTGTAGCCAACACACACGGTTATTG
+GTGTGGATCAATAGTTTATACTTTTAAATTTGTTAAGACTCAATTTCATTCTGGACGTTTACGCATTAGT
+TTTATTCCATTTTATTATAATACGACTATATCTGCAGGAGTTCCCGATGTTTCTCGTACCCAAAAAGTAA
+TCGTTGATCTGCGCACCTCTACAGAAGTCTCTTTCACTATTCCGTATGTGTCTTCACGACCTTGGATGTA
+CTGTATTCGTCCTGAAGCTTCGTGGCTTGGAACCGATAATGCTTTGATGTACAACGCCGTTACGGGTATA
+GTGAGAGTTGAGGTTCTTAACCAGTTGGTTGCCGCTAACAACGTGTTTCAATCTATAGACACTATTGTTG
+AAGTTAGTGGTGGTCCTGATTTAACTTTTGCAGCACCAATGGCTCCCTCTTATGTTCCTTATTCTGGAGG
+TTTTACTTTAGCAGATGATGCGGCAGCAAAGAAACAGCGTGAGGAGGAGTATGACAACAACATACCTCAA
+ACTATTTCTAATCGTGGAAAACGTGAGGTTGAAGATGCTCGTATTGTTGCGCAAGTAATGGGTGAAGATT
+TAGCTATTCAAAGAAACGATGCTCAACATGGTGTTCATCCAATGACTATAGACACTCATAAGATCGACTC
+AAATTGGTCTCCGGAAGCGCATTGTATTGGTGAAAAGATTATGTCTATTCGCCAATTGATTAAGCGTTTT
+GGCATGGCTTTGAACTCCTTGAATTTGATAAGTGATGCACCAAACACCTTGATAGCACCATTTTCAGTTC
+AGCACCCAACTCCTGTTGTTGCCCCTGCTGAACCCATGTCCCTTTTTGAATATTATTATTTCATTTATGG
+ATTTTGGAGAGGTGGCATGAGATTTAAACTTCAGGCAGTACGTACAAACTCAGCAGAAACATCAGTTAAA
+ACCGACACAACTTGGACTGTAAATTTGTGGAATTCTGTACAAGATTCTTTTAATTCTCTAATTAATGTAT
+TTAGTACTACTGATTACCCTATAAAATCCACAGGAGCACTTCCAGCCGGAACAAGCGGTTTTGGCAATTC
+GATGACGTATATAGATCCTGAGGTTGAAGGTTTTATGGAATTTGAGATTCCATATTATAATATCTCCCAT
+ATTTCTCCAGCTACAACCTATGTTCGTGGTACTGAATCTCCTATTACAATTAATAGTGTCTTGCGTGGAC
+ATTTGCCACCACAAATTGTGGCTGTTGCACCACAGGGCACTATTGCCACTACAGATGTAGTGAACGCTCA
+ATTTGCTCGTGCTCCTTCTGACGACTTTTCATTTATGTATCTCGTTGGTGTTCCACCACTTACCAACGTC
+GCTCGTCCCTAACTCCCTTACTATTCTGGATCCTTTAAAATTTATTAGGATAGACAAAAATTAACTCTAT
+ATTAGATAGTATTAGATTAAGTTTCTTTTTGGTTTTGGGTTTTATTCAGTAACTATCTGCCCTGCTTACA
+CGGGTATTATTTTTAATTCTTGTCCCTTCTGGACTCTTTTATTTTGTATTTTCAAAATTTTTACTAATTT
+TTAGTCAGAGTCCTTAGGGGCTACCAGGTTTTTCGCAATTTTCCTGCTTACTGACAGTAATTGCAATTTC
+GAATTAAAATAATAGTTGTTTTCT

resources/h3n2_ha/gffs/h3n2_ha.gff3

@@ -0,0 +1,5 @@
+##gff-version 3
+##sequence-region EPI1857216 1 1718
+EPI1857216  feature gene    1   48  .   +   .   gene_name="SigPep"
+EPI1857216  feature gene    49  1035    .   +   .   gene_name="HA1"
+EPI1857216  feature gene    1036    1698    .   +   .   gene_name="HA2"