Pandaseq

Introduction

Pandaseq is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

For more information, please check its | Docker hub: https://hub.docker.com/r/pipecraft/pandaseq and its home page on Github.

Versions

2.11

Commands

pandaseq

Module

You can load the modules by:

module load biocontainers
module load pandaseq

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 Pandaseq on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=pandaseq
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers pandaseq

pandaseq -f SRR069027_1.fastq -r SRR069027_2.fastq