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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/2.4.2
$ 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
$ tar xf 2.4.2.tar.gz
$ cd Flye-2.4.2
$ mkdir -p /export/apps/flye/2.4.2
$ chown aorth /export/apps/flye/2.4.2
$ python2 -m virtualenv /export/apps/flye/2.4.2
$ source /export/apps/flye/2.4.2/bin/activate
$ python build
$ python install
$ sudo chown -R root:root /export/apps/flye/2.4.2
flye-software.1554928729.txt.gz · Last modified: 2019/04/10 20:38 by aorth