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Updated Oct 19, 2026

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Check contig naming before combining genomic files

genomic-contig-check is an offline contig-naming and assembly-compatibility checker.

Agent
Catch chromosome-name mismatchesCheck reference compatibilityKeep uncertain assembly hints visible

overview

What genomic-contig-check does

Identify the genome assembly and contig naming behind BED/GTF/GFF3/VCF/FASTA-index/sizes files and check that they can be joined (chr-prefix and assembly mismatches) with K-Dense's genomic-coordinates check_contigs. JSON report; offline.

Compare 1 to 10 BED, GTF, GFF3, VCF, FASTA-index or chromosome-size files, optionally against reference genome sizes. Return JSON with per-file contig information, naming styles, assembly hints, incompatibilities and the script log.

Paths must stay within the supplied folder; the limit is 1 GiB per file. Assembly hints use a built-in primary-chromosome length table. Interval coordinates alone are often ambiguous. Incompatible or unidentifiable inputs are successful report data with compatible false; invalid paths and usage fail.

Packaged version: 065b734. Upstream license: MIT.

source github.com/k-dense-ai/scientific-agent-skills/tree/065b734670d7d990627dbc06a05b5a99be33f1f1/skills/genomic-coordinates

use cases

Where genomic-contig-check fits

Catch chromosome-name mismatches

Compare plain 1 and chr1 naming before a join.

Check reference compatibility

Include chromosome sizes or a FASTA index as the reference.

Keep uncertain assembly hints visible

Distinguish a recognizable length table from ambiguous interval-only evidence.

reference

genomic-contig-check inputs and flags

3 inputs
NameTypeFlagDescription
sourceFOLDER--sourceFolder holding the genomic files to compare.
filesSTRING--filesComma-separated paths inside the folder (1–10), e.g. variants.vcf,annotation.gtf,ref.fa.fai; each at most 1 GiB.
genomeSTRING--genomeOptional chrom.sizes or .fai path inside the folder to compare every file against.

Showing key inputs. genomic-contig-check exposes 3 inputs in total.

example

Run genomic-contig-check

genomic-contig-check · command
python3 /app/run.py --source ./source --files nochr.bed,chr.bed --genome hg38.sizes ./output

guidance

Choosing genomic-contig-check

Use genomic-contig-check before joining files that may mix chr-prefixed and plain contigs. It does not rewrite names, lift coordinates between assemblies or prove the correct assembly for an arbitrary interval file. Interval validation and set arithmetic are separate jobs.

faq

genomic-contig-check questions

source: Folder holding the genomic files to compare. files: Comma-separated paths inside the folder (1–10), e.g. variants.vcf,annotation.gtf,ref.fa.fai; each at most 1 GiB. genome: Optional chrom.sizes or .fai path inside the folder to compare every file against.

Compare 1 to 10 BED, GTF, GFF3, VCF, FASTA-index or chromosome-size files, optionally against reference genome sizes. Return JSON with per-file contig information, naming styles, assembly hints, incompatibilities and the script log.

Paths must stay within the supplied folder; the limit is 1 GiB per file. Assembly hints use a built-in primary-chromosome length table. Interval coordinates alone are often ambiguous. Incompatible or unidentifiable inputs are successful report data with compatible false; invalid paths and usage fail.

Use genomic-contig-check before joining files that may mix chr-prefixed and plain contigs. It does not rewrite names, lift coordinates between assemblies or prove the correct assembly for an arbitrary interval file. Interval validation and set arithmetic are separate jobs.

The public image repository gives immutable image and ORAS download commands, the expected source/notices bundle checksum and pinned upstream source directions. The accompanying OCI bundle retains the original build recipe, runtime sources and full installed notices. The Git recipe keeps primary notices and an exact layer/hash index; it does not duplicate the full installed notice tree or mirror every upstream source archive. Image, source and license notice downloads.

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Run genomic-contig-check yourself

The saved fixture verifier confirmed GRCh38/hg38 from reference lengths and a mismatch between plain and chr-prefixed BED contigs. The complete native JSON was not retained. The command shows the container entrypoint with example paths.

Open genomic-contig-check in the libraryBuild a workflow with it

Facts on this page come from the live Trickest tool library.