Tiled amplicon RT-PCR followed by sequencing with Illumina or Oxford Nanopore technology is the most popular method for generating SARS-CoV-2 whole genome sequences. Use of tiled amplicon sequencing allows samples with low viral genome copy number or degraded RNA to be assembled, but requires some modifications to standard NGS assembly protocols.
This article outlines a workflow for assembly of SARS-CoV-2 sequences from Illumina data, including quality trimming and removal of amplicon primers, map to reference, SNP calling and consensus generation. The workflow requires the BBDuk plugin, this can be installed by going to Tools > Plugins.
This workflow has been tested on publicly available datasets from the NCBI SRA, projects PRJNA627229 (Walker et al, 2020) and PRJNA622817 (Paden et al, 2020), and gives identical results to the iVar pipeline (Grubaugh et al., 2019) and the CDC analysis pipeline for Illumina multiplex PCR.
1. Quality trimming and removal of amplicon primer sequences.
Prior to assembly it is important to remove poor quality bases and the PCR primers used to generate the tiled amplicons. If the primer binding site in the genome contains mismatches to the primer, variants in those regions may be missed if the primer sequences are not removed prior to assembly and variant calling.
The BBDuk plugin with some modified settings can be used to do both quality trimming and removal the amplicon primers in a single step. For paired end sequences which have not been merged, the amplicon primer is located at the 5’ end of each read. Prior to running BBDuk, the set of primer sequences used in sequencing must be imported into Geneious so these can be selected for adapter trimming. A guide to importing Artic network and other tiled amplicon sequencing primer sets from CSV or TSV files is at this link.
Once your primers have been imported into Geneious, open BBDuk by going to Annotate and Predict > Trim with BBDuk. Under Adapters, select the folder containing the primer sequences, and set Trim to Left End. Adjust the Kmer Length and Maximum Substitution settings as shown in the screenshot below. To ensure only forward facing primers at the start of the read are trimmed, add the following custom commands under More Options:
To trim off low quality bases and filter out short reads, set Trim Low Quality to 30, and Discard Short Reads to 75 bp.
2. Map to Reference
The reference genome for SARS-CoV-2 can be obtained from NCBI, accession MN908947.
To map your trimmed reads to this sequence, select the file of trimmed reads and open Map to Reference under the Align/Assemble button. Set the reference sequence in the reference chooser, and set Sensitivity to Low, and Fine tuning iterations to 3.
3. Consensus sequence generation
The preferred method for consensus sequence generation is to call variants on the assembled reads and then apply those variant bases to the reference sequence, rather than generating a consensus directly from the assembly. This ensures that only statistically significant variants with good coverage depth are included in the consensus sequence.
To call variants, select the contig assembly document produced by Map to reference and go to Annotate and Predict > Find Variations/SNPs. Set Minimum Coverage to 100, and turn off Minimum Strand Bias P-value. If the strand bias setting is left on some variants may be missed, as the tiled amplicon approach can result in portions of the genome covered by only forward or reverse reads.
After the SNP calling has been completed, save the results and then go to Workflows->Apply Variants to Reference to generate a new consensus sequence containing the variant bases.
Automated Workflow for Geneious Prime 2012.1.2 and above
The analysis pipeline described here has been combined into a Geneious Workflow, attached below.
To import the workflow into Geneious, drag and drop it onto the Geneious window. Then go to Manage Workflows, select the workflow and go View/Edit. Open each step of the workflow by clicking on the step and going View/Edit options. This will update the options for your copy of Geneious and enable you to select the primers and reference sequence from your own database.
To run the workflow, close the Manage Workflows window and select the files of raw Illumina reads you wish to assemble. Then click the Workflows button and select the workflow from the list.