SARS-CoV-2 Genomic Surveillance and RNASeqAnalysis

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

1. Variant Surveillance
2. Epitope Surveillance

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Variant Surveillance

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

Run with:

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.

Website

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

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Epitope Surveillance

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

Example command line to run script:

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

The program should run with Python 3.6 or later

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

Possible Errors:

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]