Flye¶
Flye is a de-novo assembler for single molecule sequencing reads. It is designed for a wide range of datasets, from small bacterial projects to large scale assemblies.
Flye is available as a module on Apocrita.
Usage¶
To run the default installed version of Flye, simply load the flye
module:
$ module load flye
$ flye --help
usage: flye (--pacbio-raw | --pacbio-corr | --nano-raw |
--nano-corr | --subassemblies) file1 [file_2 ...]
--genome-size SIZE --out-dir PATH
[--threads int] [--iterations int] [--min-overlap int]
[--meta] [--plasmids] [--no-trestle] [--polish-target]
[--debug] [--version] [--help] [--resume]
[--resume-from] [--stop-after]
For usage documentation, run flye --help.
Core Usage
To ensure that Flye always uses the correct number of cores, the
--threads=${NSLOTS} option should be used.
Example job¶
Serial job¶
Here is an example job running on 4 cores and 16GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 4
#$ -l h_rt=1:0:0
#$ -l h_vmem=4G
module load flye
# Run flye on raw Oxford Nanopore reads with a 325M genome size,
# intermediate output and final assembly written to outdir
flye --nano-raw data.fq.gz \
--genome-size 325M \
--out-dir outdir \
--threads ${NSLOTS}