====== 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
* Added: April, 2019
* Updated: December, 2021
* Link: https://github.com/fenderglass/Flye
===== Usage =====
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 [[https://github.com/fenderglass/Flye/blob/flye/docs/USAGE.md|the documentation]] for more information.
===== Installation ======
Notes from the sysadmin during installation:
$ cd /tmp
$ wget https://github.com/fenderglass/Flye/archive/2.9.tar.gz
$ 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 setup.py 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.