FADE(Fragmentase Artifact Detection and Elimination) is a method of identification and removal of enymatic fragmentation artifacts.

Features

• fade accepts SAM/BAM/CRAM files containing reads that have been mapped to a reference genome and filters or cleans up artifact-containing reads according to the following procedure.
• The annotate subcommand performs the initial analysis and adds BAM tags encoding information concerning artifact status to the alignments, used during filtration to remove the artifacts.
• The out subcommand eliminates the artifact. It either removes reads from the output BAM/SAM file completely if they or their mate contain an identified fragmentation artifact or artifact-containing reads are trimmed to remove extraneous sequence originating from the opposite strand.
• The stats subcommand reports extended information on all reads identified by annotate to contain the artifact.
• The stats-clip subcommand reports information on all soft-clipped sequences present.
• The extract subcommand allows the extraction of the artifact sequences in their remapped state.

References:

• Thomas Gregory, Apollinaire Ngankeu, Shelley Orwick, Esko A Kautto, Jennifer A Woyach, John C Byrd, James S Blachly Characterization and mitigation of fragmentation enzyme-induced dual stranded artifacts NAR Genomics and Bioinformatics, Volume 2, Issue 4, December 2020, lqaa070, https://doi.org/10.1093/nargab/lqaa070 PubMed |  Journal

• fade Main Site:Main Site

• Module Name: fade (see the modules page for more information)
• fade is easy to run:

  	fade -h

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --cpus-per-task=2 --mem=4G
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load fade
[user@cn3144 ~]$ mkdir -p /data/$USER/fade; cd /data/$USER/fade
[user@cn3144 fade]$ fade -h
Fragmentase Artifact Detection and Elimination
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.

[user@cn3144 fade]$ fade annotate
Fragmentase Artifact Detection and Elimination
annotate: performs re-alignment of soft-clips and annotates bam records with bitflag (rs) and realignment tags (am)
usage: ./fade annotate [BAM/SAM input] [Indexed fasta reference]

-t     --threads extra threads for parsing the bam file
    --min-length Minimum number of bases for a soft-clip to be considered for artifact detection
-w --window-size Number of bases considered outside of read or mate region for re-alignment
-b         --bam output bam
-u        --ubam output uncompressed bam
-h        --help This help information.

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
#SBATCH --job-name=S1_fade
#SBATCH --output=S1_fade.out
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem=4Gb
#SBATCH --time=2:00:00
#SBATCH --partition=norm

set -e
module load fade
cd /data/$USER/fade
fade annotate -t 8 -b sam1.bam ref.fa > sam1.anno.bam

Submit the job:

sbatch fade.sh

Create a swarmfile (e.g. fade.swarm). For example:

fade annotate -t 8 -b sam1.bam ref.fa > sam1.anno.bam
fade annotate -t 8 -b sam2.bam ref.fa > sam2.anno.bam
fade annotate -t 8 -b sam3.bam ref.fa > sam3.anno.bam

Submit this job using the swarm command.

swarm -f fade.swarm -g 8 --module fade