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Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Flye also includes a special mode for metagenome assembly.



See which versions of flye are available:

$ module avail flye

Load one version into your environment and run it:

$ module load flye/2.9
$ flye

Note: you can control the number of CPU threads used by flye with the –threads option. See the documentation for more information.


Notes from the sysadmin during installation:

$ cd /tmp
$ wget
$ tar xf 2.9.tar.gz
$ cd Flye-2.9
$ sudo mkdir -p /export/apps/flye/2.9
$ sudo chown aorth /export/apps/flye/2.9
$ python3 install --prefix=/export/apps/flye/2.9
$ sudo chown -R root:root /export/apps/flye/2.9

Note: I tried to install this using a python3 virtual environment but it gave me strange errors. As flye doesn't actually need any third-party Python packages I installed it in its own prefix without a venv.

flye-software.txt · Last modified: 2021/12/27 16:00 by aorth