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Flye is a de-novo assembler for single molecule sequencing reads. It is designed for a wide range of datasets, from small bacterial projects to large scale assemblies.

Flye is available as a module on Apocrita.


To run the default installed version of Flye, simply load the flye module:

$ module load flye
$ flye --help

usage: flye (--pacbio-raw | --pacbio-corr | --nano-raw |
         --nano-corr | --subassemblies) file1 [file_2 ...]
         --genome-size SIZE --out-dir PATH
         [--threads int] [--iterations int] [--min-overlap int]
         [--meta] [--plasmids] [--no-trestle] [--polish-target]
         [--debug] [--version] [--help] [--resume]
         [--resume-from] [--stop-after]

For usage documentation, run flye --help.

Core Usage

To ensure that Flye always uses the correct number of cores, the --threads=${NSLOTS} option should be used.

Example job

Serial job

Here is an example job running on 4 cores and 16GB of memory:

#$ -cwd
#$ -j y
#$ -pe smp 4
#$ -l h_rt=1:0:0
#$ -l h_vmem=4G

module load flye

# Run flye on raw Oxford Nanopore reads with a 325M genome size,
# intermediate output and final assembly written to outdir
flye --nano-raw data.fq.gz \
     --genome-size 325M \
     --out-dir outdir \
     --threads ${NSLOTS}