{% extends 'sharedTemplates/base.html' %} {% block title %}VDJ-Insights{% endblock %} {% block body %}

Command-Line Arguments

Summary of the required and optional arguments for the V(D)J annotation tool.

Argument Description
-r, --receptor-type Type of receptor to analyze. Choices: IG (immunoglobulin) or TR (T-cell receptor). Required when using --default.
-i, --input
or
-a, --assembly
--input: directory containing extracted sequence regions (already isolated from an assembly)
--assembly: directory containing a complete genome assembly
-l, --library Path to the FASTA library file containing reference V(D)J segment sequences.
-f, --flanking-genes Comma-separated list of flanking genes in JSON format. For a single flanking gene, use "-" as a placeholder.
-s, --species Scientific species name (e.g., Homo sapiens).
-M, --metadata Path to the metadata file (.xlsx). Download example template here.
-o, --output Output directory for the results (default: annotation_results).
-m, --mapping-tool Mapping tool(s) to use: minimap2, bowtie, bowtie2 (default: all).
-t, --threads Number of threads for parallel processing (default: 8).
--default Use default settings. Cannot be used together with --flanking-genes.
-S, --scaffolding Path to reference genome (FASTA). Only supported for phased assembly files.

Used command

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{{ col }}
{{ row[col] }}{{ row[col] }}
{% endblock %}