VirAmp-Hub

A tool that lets you manipulate/convert viral amplicon/primer scheme information.

What is it for?

The layout of (tiled-) amplicon schemes for amplifying and sequencing viral genomes is typically specified through one of a number of non-standardized scheme files. These can, generally, not be used interchangeably with downstream analysis tools.

VirAmp-Hub can convert between commonly used scheme file formats, such as used, e.g., by the ARTIC network, the ivar and cojac suites of tools, and Galaxy tools and workflows for viral sequencing data analysis.

Usage

After installation (pip install viramp-hub), use the package via the scheme-convert command.

For help run:

scheme-convert --help

Prepare an existing primer scheme file for use with ivar:

scheme-convert primer_scheme.bed --to bed --bed-type ivar -o ivar.bed

Generate an amplicon insert scheme file for cojac:

scheme-convert primer_scheme.bed --to bed --bed-type cojac -o cojac_insert.bed

Generate an amplicon info file for use with ivar inside Galaxy:

scheme-convert primer_scheme.bed --to amplicon-info -o info.tsv

Amplicon info files are simple tab-separated files listing primers contributing to the same amplicon on a single line. For nested primer schemes, you can control, which primers to report in the info file.

List only the inner primers:

scheme-convert primer_scheme.bed --to amplicon-info -r inner -o info.tsv

List only the outer primers:

scheme-convert primer_scheme.bed --to amplicon-info -r outer -o info.tsv

VirAmp-Hub tries to autodetect primer to amplicon assignments using the Python re pattern: r'(?P<prefix>(.*_)*)(?P<num>\d+).*_(?P<name>L(?:EFT)?|R(?:IGHT)?)'. If this fails for any given primer scheme, it is possible to override autodetection by providing an amplicon info file directly, e.g.:

scheme-convert primer_scheme.bed -a amplicon_info.tsv --to bed --bed-type cojac -o cojac_insert.bed

or:

scheme-convert primer_scheme.bed -a amplicon_info.tsv --to amplicon-info -r inner -o info.tsv