Alfred

Introduction

Alfred is an efficient and versatile command-line application that computes multi-sample quality control metrics in a read-group aware manner.

For more information, please check its website: https://biocontainers.pro/tools/alfred and its home page on Github.

Versions

• 0.2.5

• 0.2.6

Commands

• alfred

Module

You can load the modules by:

module load biocontainers
module load alfred

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 Alfred on our clusters:

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

module --force purge
ml biocontainers alfred

alfred qc -r genome.fasta -o qc.tsv.gz sorted.bam