Analyzing Illumina SARS-CoV-2 sequencing data (ARTICplus method)

Nephele's SARS-CoV-2 pipeline supports the ARTICplus method, which is designed to analyze data from pooled, tiled, multiplexed libraries. The pipeline can work with primer designs such as NEB's VarSkip, IDT's Midnight, and ARTIC. For more information, please refer to the SARS-CoV-2 pipeline user guide.

This tutorial outlines the steps for running the ARTICplus method pipeline starting from raw fastq files.

Step 1: Select pipeline and upload files

1. Go to step 2 “Analyze”, select "Viral genomics" and hit "Start job" button
2. Select ARTICplus paired or single end
3. Upload files

Step 2: Submit job

1. Select from among the various primer schemas available. Please note: make sure it's the same as what you used in library preparation. Alternatively, upload a .bed format primer file.
2. Give a name to the job and opt to receive alignment files (.bam format)
3. Proceed to “Validate and Submit”. A job ID will be assigned.
4. Nephele will send an e-mail with a link to the log file. (Optional): Monitor progress of job by going to the link provided on the “Nephele job” e-mail.

Step 3: View results and explore bam files

1. Download results folder from the link provided on the email with subject “Nephele job”
2. Explore output files: metrics, results, alignment (.bam), consensus (.fasta). The reports folder contains a text file with the number of mutations for each sample. In addition, the metrics folder contains coverage plots files (.coverage_plot.pdf) for each sample. (Optional): View alignment and confirm primer masking of reads by uploading the bam files to a browser.

Step 4: Explore consensus sequence

1. Open genome file (.fasta) in a text editor
2. Use consensus genome as input for tools such as Pangolin or Nextclade to assign lineage and clade information.