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README.md

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+# 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](https://github.com/artic-network/primer-schemes),
+the [ivar](https://github.com/andersen-lab/ivar) and
+[cojac](https://github.com/cbg-ethz/cojac) suites of tools, and
+[Galaxy](https://galaxyproject.org/) 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
+