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VPrimer

A method of designing and updating primer and probe with high variant coverage for RNA virus detection

1. Get VPrimer

To get VPrimer, follow the queries.

$ git clone https://github.com/qhtjrmin/VPrimer.git

The source codes are in "src" folder. Since the VPrimer consists of several steps, the vPrimer must be executed using a different input for each step. The guidline for execution is in section 2.

Environment

VPrimer needs the following softwares to run in the system:

  • CUDA toolkit version 8 or higher.
  • Nvidia driver (v384 or higher)
  • gcc/g++ 4.8.x or later

#2. Running

2.1 Prepare input sequence data

The example of input files that can be used are in "input_test" folder. In the case of host data, it should be decompressed as the following command to use for input.

$ gunzip human_host.txt.gz

The required data is as follow:

  • host sequence
  • virus sequence
  • mapping data for virus sequence (oid-vidset, sid-oid, sid-vidset)

The mapping data is for coverage checking and homology test against other virus. Refer to test inputs and the paper for the format and meaning of the files.

2.2 Input data generation

Refer to the following link: https://github.com/Hajin-Jeon/VPrimer-input-generator

2.3 Get VPrimer execution file and run

The basic execution order is as follows.

  • find host subsequences (host_primer and host_probe)
  • find virus primer and probe candidates (virus_primer and virus_probe)
  • variant coverage filtering: filter out sequences under 95% coverage (check_coverage)
  • find primer pair having at least one proper probe (primer_pair)
  • find final primer-probe sets (final_set)

You can run additional check_coverage, referring to the paper.