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