====== Flye ======
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.

===== Information =====

  * Version: 2.9.6
  * Added: April, 2019
  * Updated: May, 2025
  * Link: https://github.com/mikolmogorov/Flye

===== Usage =====

See which versions are available:
<code>$ module avail flye</code>

Load one version into your environment and run it:
<code>$ module load flye/2.9.6
$ flye</code>

Note: you can control the number of CPU threads used by flye with the ''--threads'' option. See [[https://github.com/fenderglass/Flye/blob/flye/docs/USAGE.md|the documentation]] for more information.

===== Installation ======

Notes from the sysadmin during installation:

<code>$ cd /tmp
$ git clone https://github.com/mikolmogorov/Flye.git -b 2.9.6
$ cd Flye
$ module load python/3.10
$ sudo mkdir -p /export/apps/flye/2.9.6
$ sudo chown aorth /export/apps/flye/2.9.6
$ python3 setup.py install --prefix=/export/apps/flye/2.9.6
$ sudo chown -R root:root /export/apps/flye/2.9.6</code>

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.