Cojac: pubmut (version 0.9.2+galaxy0)

Co-occurrence results generated by mutbamscan:

The tool can work with json- or yaml-formatted output of cojac mutbamscan.

Available amplicon and lineage annotations:

For best readability of its report the tool requires a per-lineage amplicon info dataset (in yaml format) produced by the mutbamscan tool and the original lineage definitions. If all you have is the per-lineage amplicon info, you can use it to obtain a nearly identical report, but cojac-internal lineage identifiers won't be translated into standard lineage names. With no available annotations a limited report can still be generated, but this is not recommended.

Combined cojac per-amplicon lineage definitions:

Source of lineage definitions:

Cojac detects lineage evidence based on lineage mutation patterns deined in tool-specific yaml format. You can choose between the (possibly outdated) definitions shipped with the tool or definitions provided as a collection of yaml datasets in your history. See the tool help below for more details.

Output formattings

Output formatting 0

What it does

The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples.

Information about cojac cooc-pubmut

The tool pretty-prints json or yaml output of cojac cooc-mutbamscan.

Hint: The output (unless you select html format) is best viewed in spreadsheet software that understands linebreaks.