====== 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: $ module avail flye Load one version into your environment and run it: $ module load flye/2.9.6 $ 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 $ 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 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.