HANSEN integrated Nanopore workflow

Lep-AMR Amplicon-based antimicrobial resistance analysis

Lep-AMR is a targeted antimicrobial-resistance analysis workflow for Mycobacterium leprae using Oxford Nanopore MinION amplicon sequencing and EPI2ME Amplicon workflow (wf-amplicon). It focuses on established resistance-associated loci in rpoB, folP1 and gyrA, supporting variant-level interpretation of rifampicin, dapsone and fluoroquinolone resistance.

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Start a new Lep-AMR run

Upload a single barcode ZIP and run the local HANSEN deployment pipeline.

Data policy: Only one barcode is allowed per upload. Each run and its associated uploaded FASTQ data are automatically deleted after 24 hours. You can also delete a completed run manually from the run page.
Upload one ZIP containing exactly one barcode folder, for example barcode17/*.fastq.gz. Multiple FASTQ files inside the same barcode folder are allowed, but multiple barcode folders are not allowed.
Use Auto-detect when you are unsure, or select a known amplicon if the barcode was sequenced for a specific target.
Previous runs
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Workflow diagram

How a single barcode FASTQ upload is processed inside HANSEN.

1

Upload ZIP

Upload one ZIP containing one barcode folder with FASTQ or FASTQ.GZ files.

2

Validate barcode

Lep-AMR rejects uploads containing more than one barcode folder.

3

Screen reads

Sampled reads are compared with rpoB, folP1 and gyrA amplicon references.

4

Select target

The best target or requested panel is selected for downstream analysis.

5

Prepare inputs

Barcode folders, sample sheet and selected reference FASTA are prepared.

6

Run EPI2ME

Nextflow launches wf-amplicon for alignment, coverage and variant calling.

7

Live logs

The run page streams the pipeline log as the analysis progresses.

8

Download/delete

Download reports, then delete the run manually or allow automatic 24-hour cleanup.

View example results