Flye

Introduction

Flye: Fast and accurate de novo assembler for single molecule sequencing reads.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/flye
Home page: https://github.com/fenderglass/Flye

Versions

2.9.1
2.9.2
2.9

Commands

flye

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run flye on our clusters:

#!/bin/bash
#SBATCH -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=flye
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load flye/XXXX ### you can run *module avail flye* to check all available versions

flye --pacbio-raw E.coli_PacBio_40x.fasta --out-dir out_pacbio --threads 12
flye --nano-raw Loman_E.coli_MAP006-1_2D_50x.fasta --out-dir out_nano --threads 12