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.

• Version: 2.9.4
• Added: April, 2019
• Updated: August, 2024
• Link: https://github.com/mikolmogorov/Flye

See which versions of flye are available:

$ module avail flye

Load one version into your environment and run it:

$ module load flye/2.9.4
$ 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
$ module load python/3.9
$ git clone https://github.com/mikolmogorov/Flye.git -b 2.9.4
$ cd Flye
$ sudo mkdir -p /export/apps/flye/2.9.4
$ sudo chown aorth /export/apps/flye/2.9.4
$ python3 setup.py install --prefix=/export/apps/flye/2.9.4
$ sudo chown -R root:root /export/apps/flye/2.9.4

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.