README
The folder example_data contains a series of example data and files 
to be used in a demonstration on how to submit 3 SARS-CoV-2 samples 
to an example project, along with raw read data and sequences associated 
with each sample. The example data was originally produced by ENA 
(https://www.ebi.ac.uk/ena/browser/home), but we have restructured 
it for use with the two submission routes described in the tutorial. 
With the example data, you can submit 3 different samples to an example 
project, together with raw read data and sequences associated with 
each sample.

The files are organised as follows:

01-route/
    01-route/runs/
        01-route/runs/pairedfastq.tsv
        01-route/runs/paired_fastq_manifest_sample1.txt
        01-route/runs/paired_fastq_manifest_sample2.txt
        01-route/runs/paired_fastq_manifest_sample3.txt
    01-route/sequences/
        01-route/sequences/hCoV-19_isolate_1_manifest.txt
        01-route/sequences/hCoV-19_isolate_2_manifest.txt
        01-route/sequences/hCoV-19_isolate_3_manifest.txt
        01-route/sequences/manifest_upload.sh

02-route/
    02-route/runs/
        02-route/runs/experiments.xml
        02-route/runs/runs.xml
        02-route/runs/submission.xml
    02-route/samples/
        02-route/samples/samples.xml
        02-route/samples/submission.xml
        02-route/samples/submission_modify.xml
    02-route/sequences/
        02-route/sequences/hCoV-19_isolate_1.json
        02-route/sequences/hCoV-19_isolate_2.json
        02-route/sequences/hCoV-19_isolate_3.json
    02-route/study/
        02-route/study/project.xml
        02-route/study/submission.xml

data/
    data/raw/
        data/raw/SARS-CoV-2-Sample1_1.fastq.gz
        data/raw/SARS-CoV-2-Sample1_2.fastq.gz
        data/raw/SARS-CoV-2-Sample2_1.fastq.gz
        data/raw/SARS-CoV-2-Sample2_2.fastq.gz
        data/raw/SARS-CoV-2-Sample3_1.fastq.gz
        data/raw/SARS-CoV-2-Sample3_2.fastq.gz
    data/samples/
        data/samples/sample_spreadsheet.tsv
        data/samples/sample_spreadsheet.xlsx
    data/sequences/
        data/sequences/hCoV-19_isolate_1.fasta.gz
        data/sequences/hCoV-19_isolate_1_chrm_list.txt.gz
        data/sequences/hCoV-19_isolate_2.fasta.gz
        data/sequences/hCoV-19_isolate_2_chrm_list.txt.gz
        data/sequences/hCoV-19_isolate_3.fasta.gz
        data/sequences/hCoV-19_isolate_3_chrm_list.txt.gz
