DNA shearing is a crucial first step in most NGS protocols for Illumina. Enzymatic fragmentation has shown in recent years to be a cost and time effective alternative to physical shearing (i.e. sonication). We discovered that enzymatic fragmentation leads to unexpected alteration of the original DNA source material. We provide fade as a method of identification and removal of enymatic fragmentation artifacts.

• Fade main page

• Module Name: fade (see the modules page for more information)

Allocate an interactive session and run the program.
Sample session (user input in bold):
Please note cellbender is compute intensive and needs sufficient memory allocation

[user@biowulf ~]$ sinteractive --mem=20g
salloc: Pending job allocation 13632637
salloc: job 13632637 queued and waiting for resources
salloc: job 13632637 has been allocated resources
salloc: Granted job allocation 13632637
salloc: Waiting for resource configuration
salloc: Nodes cn4308 are ready for job

[user@cn4308]$ module load fade
[+] Loading fade  0.6.0  on cn4282 
[+] Loading singularity  4.0.1  on cn4282 

[user@cn4308]$ fade -h 
Fragmentase Artifact Detection and Elimination
version: v0.6.0

usage: fade [subcommand]
    annotate: marks artifact reads in bam tags (must be done first)
    out: eliminates artifact from reads(may require queryname sorted bam)
    stats: reports extended information about artifact reads
    stats-clip: reports extended information about all soft-clipped reads
    extract: extracts artifacts into a mapped bam

-h --help This help information.                                    

Create a batch input file (e.g. fade.sh). For example:

#!/bin/bash

module load fade
  
fade annotate -b sam1.bam ref.fa > sam1.anno.bam

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] fade.sh