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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.
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