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The assembly module of nanopype provides different tools to directly build consensus sequences from long read sequencing runs. Assemblies are made from the output of multiple flow-cells with names provided via a runnames.txt in the processing directory. The command to assemble contigs with Flye using Guppy for basecalling would be:

snakemake --snakefile /path/to/nanopype/Snakefile assembly/flye/guppy/WA01.fasta

The tag WA01 is arbitrary and may describe a corresponding experiment or cell line.

NOTE: The assembly module is currently not automatically tested on Travis-CI.

Folder structure

The assembly module can create the following file structure relative to the working directory:

   |--flye/                     # Flye assembler
      |--guppy/                 # Guppy basecalling
            |-- ...             # Assembler specific files
         |--WA01.fasta          # Polished Contigs
   |--wtdbg2/                   # wtdbg2 assembler
      |--guppy/                 # Guppy basecalling
            |-- ...             # Assembler specific files
         |--WA01.fasta          # Polished contigs


The assembly module does not have automatic clean up rules at the moment.


Depending on the application you can choose from one of the following assemblers, listed with their associated configuration options. All tools share the following configuration options:

threads_asm: 4
asm_genome_size : '48k'


Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies.

asm_flye_preset : '--nano-raw'
asm_flye_flags : '--asm-coverage 35'


Wtdbg2 is a very fast de novo assembler for PacBio and Oxford Nanopore reads.

asm_wtdbg2_preset : 'ont'
asm_wtdbg2_flags : ''


Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin and Pavel Pevzner, Assembly of Long Error-Prone Reads Using Repeat Graphs, Nature Biotechnology, 2019 doi:10.1038/s41587-019-0072-8

Ruan, J., Li, H. Fast and accurate long-read assembly with wtdbg2. Nat Methods 17, 155–158 (2020).