fibertools is a rust-based command line tool for creating, filtering, interacting, and extracting from Fiber-seq BAM files.

References:

• Jha, A., Bohaczuk, S. C. et al. DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools. Genome Research. 2024.

• fibertools Main Site
• fibertools Github

• Module Name: fibertools (see the modules page for more information)
• Multithreaded and GPU capable. Please set --threads to $SLURM_CPUS_PER_TASK.
• Test data in $FIBERTOOLS_TEST_DATA

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

[user@biowulf]$ sinteractive --mem=8G --cpus-per-task=4
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 fibertools

[user@cn3144 ~]$ cp $FIBERTOOLS_TEST_DATA/ctcf.bam 

[user@cn3144 ~]$ ft validate --threads 2 ctcf.bam
[00:00:01]    Records 1,770.9125/s    Read 1,879 records   Total reads tested: 1879
Fraction with m6A: 100.00%
Fraction with nucleosomes: 100.00%
Numer of FIRE calls: 4229
Fraction aligned: 100.00%
Fraction phased: 0.00%
Fraction with kinetics: 0.00%

Fiber-seq BAM file is valid
[user@cn3144 ~]$ ft qc ctcf.bam
[00:00:01]    Records 1,715.7719/s    Read 1,879 records                                                                                      statistic	value	count
phased_reads	UNK	1879
phased_bp	UNK	22370158
fiber_length	1543	1
fiber_length	1772	1
fiber_length	1839	1
fiber_length	1848	1
fiber_length	1932	1
fiber_length	1967	1
fiber_length	2240	1
[...]

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

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

#!/bin/bash
set -e
module load fibertools
cd /data/$USER/project-directory
ft extract --threads $SLURM_CPUS_PER_TASK --m6a m6a.bed.gz input.bam 

Update paths and filenames as needed. Submit this job using the Slurm sbatch command.

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

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

ft predict-m6a --threads $SLURM_CPUS_PER_TASK input1.bam out1.bam
ft predict-m6a --threads $SLURM_CPUS_PER_TASK input2.bam out2.bam
ft predict-m6a --threads $SLURM_CPUS_PER_TASK input3.bam out3.bam
ft predict-m6a --threads $SLURM_CPUS_PER_TASK input4.bam out4.bam

Submit this job using the swarm command.

swarm -f fibertools.swarm [-g #] [-t #] --module fibertools