fiberhmm is a Fiber-Seq tool for calling chromatin footprints and methylase-sensitive patches (MSPs).

It works with Fiber-seq (m6A via Hia5) and DAF-seq (deamination via DddA/DddB), producing fibertools-compatible BAM output with ns/nl/as/al tags. FiberHMM provides a unified framework for calling footprints across different single-molecule chemistries (Hia5, DddA, DddB) and sequencing platforms (PacBio, Nanopore), making it straightforward to directly compare chromatin accessibility measurements between experiments.

• fiberhmm Main Site
• fiberhmm Github

• Module Name: fiberhmm (see the modules page for more information)
• Multithreaded. Please set --threads to $SLURM_CPUS_PER_TASK.
• Pre-trained models are located in $FIBERHMM_MODELS

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

[user@biowulf]$ sinteractive --mem=8G
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 fiberhmm

[user@cn3144 ~]$ cd /data/$USER/my-fiberseq-project

[user@cn3144 ~]$ fiberhmm-extract -i input.bam 
Input: input.bam
Output: /data/$USER/my-fiberseq-project
Extract types: footprint, msp, m6a, m5c
Cores: 1

=== Extracting footprint ===
Indexing input BAM...
Processing 493 regions with 1 cores...
  Regions: 493/493 | Reads: 1,879 | Features: 109,132 | 691 reads/s
Concatenating results...
Sorting BED...
Completed in 2.8s: 1,879 reads -> 109,132 features
[...]

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

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

#!/bin/bash
set -e
module load fiberhmm
cd /data/$USER/my-fiberseq-project
fiberhmm-probs \
    -a accessible_control.bam \
    -u inaccessible_control.bam \
    -o probs/ \
    --mode pacbio-fiber \
    -k 3 4 5 6 \
    --stats

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

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

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

fiberhmm-apply -i input1.bam -m model.json -o output1/ -c $SLURM_CPUS_PER_TASK
fiberhmm-apply -i input2.bam -m model.json -o output2/ -c $SLURM_CPUS_PER_TASK
fiberhmm-apply -i input3.bam -m model.json -o output3/ -c $SLURM_CPUS_PER_TASK
fiberhmm-apply -i input4.bam -m model.json -o output4/ -c $SLURM_CPUS_PER_TASK

Submit this job using the swarm command.

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