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 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.