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'Winnowmap is a long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences.' (

To align the reads of one flow cell against reference genome hg38 with guppy basecalling and aligner winnowmap run from within your processing directory:

snakemake --snakefile /path/to/nanopype/Snakefile alignments/winnowmap/guppy/WA01/batches/20180101_FAH12345_FLO-MIN106_SQK-LSK108_WA01.hg38.bam

Build and Install

Winnowmap is not installed through the pipelines build system and therefore not available within singularity/docker installations. Please refer to the winnowmap github for installation instructions and adjust the binary paths in the site.yaml inside of the winnowmap plugin folder.

Folder Structure

The winnowmap plugin integrates the winnowmap aligner with an output sam stream into the pipeline. A meryl-index rule pre-computes the kmer frequencies for the used reference genome. Please also refer to the alignment module for further documentation.

   |--winnowmap/                                             # Winnowmap alignment
      |--guppy/                                              # Using guppy basecalling


If provided, the winnowmap plugin will use the following config keys from nanopype.yaml:
  • alignment_meryl_k: 15
  • alignment_winnowmap_flags: '-ax map-ont'

Please note, that the kmer length is only used once during index creation, if you wish to update it, delete the .meryl and .meryl.txt folder and file respectively.


If you use the winnowmap plugin, please cite:

Chirag Jain, Arang Rhie, Haowen Zhang, Chaudia Chu, Brian Walenz, Sergey Koren and Adam Phillippy. "Weighted minimizer sampling improves long read mapping". Bioinformatics (ISMB proceedings), 2020.