4. Output

The pipeline produces two main outputs:

• a report <run_name>_report.txt which contains QC_status, pangolin lineage, nextclade strain, specific mutations and other QC data.
• In the directory 003_consensusFasta, the consensus.fasta files will be placed both separately and as one multi-fasta file, which can be used for downstream analysis, such as tree visualisation in clades.nextstrain.org/ or for upload to GISAID (provided they have passed QC).

Run report

The report is structured as follows:

1. Columns 1-7 shows a summary of the most interesting data from the three reports in 2-3:
2. Column 7-17 shows the full report from the QC
3. Columns 18-23 shows the full output report from pangolin
4. Columns 24- shows the full output report from nextclade

Output folder details

The output will be stored with the following structure:

• 001_rawData/
  • fast5_pass/
  • fastq_pass/
• 002_articPipeline/
  • articGuppyPlex/
  • articMinIONNanopolish/
  • qc_pass_climb_upload/
  • qc_plots/
  • <run_name>.qc.csv
• 003_consensusFasta/
  • one <run_name>_<barcode[0-9][0-9]>.consensus.fasta file for each barcode
  • one <run_name>_sequences.fasta file containing all of the QC passed consensus.fasta files
• 004_pangolin/
  • lineage_report.csv
• 005_nextclade/
  • <run_name>_sequences.fasta_nextclade.csv
• <run_name>_report.txt