GraphV - An RNA virus strain-level identification tool using long reads and genome graph.

E-mail: heruiliao2-c@my.cityu.edu.hk

Version: V1.0

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Dependencies:

• Python >=3.6
• GraphAligner 1.0.11 (https://github.com/maickrau/GraphAligner)

Make sure these programs have been installed and added in path.

Install (Only for linux or ubuntu)

git clone https://github.com/liaoherui/GraphV.git

Then, you need to download the genome graph database of 8 RNA viruses. Run:
cd GraphV
sh download.sh

If you fail to download database with download.sh, try another script then, Run:
cd GraphV
sh download_2.sh

Still failed, please email to the author to get the database.

Usage

Use python GraphV.py -h to check the usage.

A demo real data of SARS-Cov-2 is included in "Data" folder, which can be uesd for test.

A running demo: (Result will be generated in the folder called "GraphV" by default)

python GraphV.py -i Data/SRR10948550_801.fastq -v SCOV2

The below table shows relationship between virus name and virus_type parameter:

Virus Name	virus_type parameter
SARS-Cov-2	SCOV2
HIV	HIV
HCV	HCV
Ebolavirus	EBV
Zika virus	ZKV
Dengue virus	DGV
Lassa virus	LSV
Enterovirus	ETVA

Output file

There will be 5 output files of GraphV.

1. *.json file --- The alignment result file from GraphAligner.

2. *_Most_possible_Strain_report.txt --- The final report generated by GraphV.

3. *_All_Cov.txt --- The GraphV result file which is sorted by the descending order of alignment coverage.

4. *_All_Cov_by_length.txt --- The GraphV result file which is sorted by the descending order of alignment length.

5. *_Unique_Cov.txt --- The GraphV result file which is sorted by the descending order of unique coverage.

Note:

For 3, 4, the meaning of each column in the file is: Strain name, alignment length, genome length, alignment coverage.
For 5, the meaning of each column in the file is: Strain name, unique alignment length, genome length, unique coverage, strain name in database.