Viral Detection with FlexTyper Search

This is an example of ways to detect pathogenic virus reads from raw fastq files.

This dataset includes a pre-made viral query file (pathogen_query.txt), and paired-end RNA-seq fastq files (MixedVirus_100_1.fq.gz and MixedVirus_100_2.fq.gz).

To generate your own query file, go to the fmformatter/ directory in the main repository.

Generate the Index

Generate the index for the files first by running:

../build/flextyper index -r MixedVirus_100_1.fq.gz -p MixedVirus_100_2.fq.gz --gz

See also: Indexing

Adjust settings ini file

The folder contains two settings files that can be used to perform the search.

Check that the path to the ini file for the index is correct

# Path to the index Props ini

Index_MixedVirus_100_index.ini

See also: Indexing

Check that the path to the query file is correct

# Path to the input Query File

queryFile = "path_query.txt"

See also: Setting Ini File

Run the search

To execute, simply type:

../build/flextyper search -c setting_1.ini -u outputFileName

Expected Output

Expected Counts for the MixedVirus_100.fq set:

Virus	Expected Count	Setting1
HIV-1	6100	4713
U21941.1 (HPV 70)	5200	4054
FR751031.1 (HPV 68b)	5200	4057