ncov-primers

ncov-primers provides a set of tools for processing a primer BED file and generating an amplicon BED file for further processing.

Installation

pip install .

Usage

After installing the package, you can run bin/create_amplicons.py:

$ create_amplicons.py --file /path/to/primer/bed
                      --output <name of output bed file>
                      --type <type of amplicons to generate>
                      --idloc <index of id location in primer name>
                      --keep

The --type argument can be one of:

• unique_amplicons (unique regions removing primers)

• full (includes primers)

• no_primers (primers are removed)

The --keep flag is used to keep a temporary directory used to construct the amplicon file. This can be used for debugging purposes.

Primer names

The primer names within the BED file require a specific format. The name is typically found in column 4 of a standard BED file. The name must contain:

* a unique integer ID

* LEFT/RIGHT to indicate the direction of the primer

* components separated by _ (underscore)

Examples of valid primer names are: ncov_1_RIGHT and ncov_22_LEFT. In this example, the --idloc argument should be set to 1 to indicate the location within name for the id (Note: 0-based index).