SARS-CoV-2 Genomic Surveillance and RNASeqAnalysis (technically DNA) has two components:

1. Variant Surveillance
2. Epitope Surveillance

Variant Surveillance is an additional component of this project to monitor the circulating variants.

python src/SarsCov2Variants.py

This will generate csv files in output/12_variants and images in output/11_regions
Note that you will need to download the tsv files from GISAID since we are not authorized to redistribute datasets from it.

https://www.usacfi.net/covid-19-surveillance.html

Epitope Surveillance aligns multiple COVID DNA sequences, trims the genes of interest, translates to protein, and identifies mutations in epitope regions. Download the entire RNASeqAnalysis folder

python main.py -i "references/Sequences/omicron_variant" -m "references/Sequences/omicron_variant"

Optional parameters:

• -i directory which contains the fasta files
• -m directory which contains the metadata files
• -ref reference genome name (Wuhan strain) the default is the name of the first genome in the input fasta file.
• -aln TRUE when the input needs alignment and FALSE when the input is already aligned
• -eps input text file that lists the epitope regions
• -loc input text file that indicates what and where are the relevant reference genes
• -g fasta file with only the reference genome
• -o output fasta file

Input files:

• sequences.fasta
• metadata.tsv
• Reference_gene_locations.txt
• NCBI Reference Sequence_NC_045512.2.fasta
• epitopes.txt

Output files:

• 01_aligned.fasta
• 02_trimmed.fasta
• 03_protein.fasta
• 04_mutations.fasta
• 05_aminoacid_replacements.csv
• 06_unique_mutations.csv
• 07_heatmap_[protein].html
• 08_table_[protein]_[#].html
• 09_mutation_geomap.html
• 10_geoplot_variants.html
• 11_regions
• 12_variants
• 13_filtered_seq_epitsurve.csv

Fasta files can be viewed using any alignment viewers, e.g. AliView

1. Running the program in Windows or Linux might yield an error when (-aln TRUE). This is because the current MUSCLE and MAFFT programs in the folder are only compatible for MAC computers.

Solution: You can download the MUSCLE/MAFFT programs compatible to your OS free online. Or you can change the input parameter (-aln FALSE), but note here that the program assumes that your input file is already aligned.

2. An error might come up when you are running in Python 2.

Solution: convert the codes into Python 2 or install Python3 (recommended)

3. An error might come up when you don't have the following python modules:

• argparse
• numpy
• pandas
• matplotlib
• itertools
• scipy
• plotly
• datetime

Solution: Install the modules using pip in the command line/ terminal: pip install [module_name]