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draugr-demultiplexing

Automates and troubleshoots sequencing run demultiplexing via draugr, B-Fabric, and bcl2fastq.

Updated May 28, 2026
Search Tags:#bioinformatics#sequencing#10x genomics#demultiplexing#b-fabric#bcl2fastq#base mask
One-click install
npx skills add https://github.com/cpanse/skills --skill draugr-demultiplexing-cpanse
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: draugr-demultiplexing
Source: https://github.com/cpanse/skills/tree/main/sequencing-pipelines/skills/draugr-demultiplexing
Command: npx skills add https://github.com/cpanse/skills --skill draugr-demultiplexing-cpanse

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve? Demultiplexing short-read sequencing runs at FGCZ involves coordinating queue monitors, B-Fabric metadata, barcode validation, bcl2fastq/bases2fastq execution, and gStore archival — a multi-step process where failures (stuck runs, wrong base masks, barcode errors) are hard to diagnose without deep system knowledge. ## Core Features & Use Cases - Run and monitor demultiplexing: Start the automated queue monitor, manually run draugr.py on a single run, or reprocess specific orders with fine-grained skip flags. - B-Fabric integration: Query order metadata, track run status transitions (PROCESSING → DEMULTIPLEXING → DEMULTIPLEXING_FINISHED/FAILED), and set custom BasesMask attributes. - Per-chemistry base masks: Reference read structures and bcl2fastq masks for all 10x chemistries (3'/5' GEX, VDJ, ATAC, Multiome, Visium, Flex), including the ATAC i5 lowercase-y gotcha and the current manual-demux workaround for cellranger-atac/arc. - Use Case: A run is stuck in "Demultiplexing" status — check the draugr logs, identify the failure, and rerun with --demux-only-mode or --reprocess-orders to recover without repeating completed steps. ## Quick Start Ask the agent to check the demultiplexing status of a sequencing run and show the latest draugr log for troubleshooting.

Frequently Asked Questions about draugr-demultiplexing

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I manually run demultiplexing on a sequencing run with draugr?▼

Run `uv run python draugr.py --run-folder /export/local/data/<RUN_FOLDER>` from the draugr repository, passing your B-Fabric login config and analysis output folder. Add `--test-mode` to skip the gStore copy and use the test B-Fabric instance.

How do I reprocess specific orders after a demultiplexing failure?▼

Use `draugr.py --run-folder <RUN> --reprocess-orders 12345,56789` with comma-delimited order IDs. Combine with flags like `--skip-rawqc` or `--demux-only-mode` to avoid repeating steps that already completed successfully.

What bcl2fastq base mask should I use for 10x Multiome ATAC libraries?▼

Multiome ATAC uses `y50n*,I8n*,y24n*,y49n*` — the i5 read is the 16bp cell barcode plus 8bp linker and must be emitted as a regular read with lowercase y. Currently draugr ignores the BasesMask override on the 10x dual-index path, so demux these lanes manually with bcl2fastq.

Why is a sequencing run stuck in Demultiplexing status in B-Fabric?▼

A stuck status usually means the draugr process crashed mid-run. Check the log at /srv/GT/analysis/falkonoe/dmx_logs/prod/<RUN_NAME>.log, fix the underlying issue, then rerun with recovery flags like `--demux-only-mode` or `--skip-demux`.

Does draugr support Element Biosciences AVITI runs?▼

Yes, draugr supports Element AVITI instruments using bases2fastq instead of bcl2fastq for demultiplexing. Illumina platforms including NovaSeq, NextSeq, MiSeq, HiSeq, iSeq, and MiniSeq are also supported.

When should I avoid setting a custom BasesMask in B-Fabric?▼

Avoid it on mixed runs, because BasesMask is global and applies to all bcl2fastq paths on the run. If a lane mixes standard samples with a special chemistry like Visium HD, leave BasesMask unset and run bcl2fastq manually for the special-chemistry path.

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