FiberHMM
Chromatin footprint calling on single DNA molecules from Fiber-seq (m6A) and
DAF-seq (deamination) data. For every read, FiberHMM calls nucleosomes,
transcription-factor and other sub-nucleosomal footprints, and the
methylase-sensitive patches (MSPs) between them, using sequence-context-aware
emission models; across molecules, it finds recurrent footprint classes and
measures how often each molecule carries them. Calls are written into the BAM
as fibertools-compatible ns/nl/as/al and Molecular-annotation MA/AQ
tags, readable by ft, FIRE and FiberBrowser.
Documentation: fiberseq.github.io/FiberHMM
(source in docs/).
FiberHMM 3.0.0 is the third generation of the FiberHMM family, released with FiberBrowser 3.0.0. Nanopore Hia5 and DddB users: the Nanopore Hia5 and DddB emission tables shipped in 2.x releases were context-swapped; re-run those calls made with 2.x.
fiberhmm-check <your outputs>lists which files need re-running. See Upgrading from 2.x and the CHANGELOG.
Install
pip install fiberhmm # Python >= 3.10
pip install "fiberhmm[all]" # plus QC figures (matplotlib) and HDF5 posteriors (h5py)
Quick start
# DAF-seq amplicons / plasmids: reads + reference in, FiberBrowser-ready calls out
fiberhmm-pipeline reads.fastq.gz --reference plasmid.dna --enzyme dddb -o run/
# Aligned BAMs
fiberhmm-call -i aligned.bam -o calls.bam --enzyme hia5 --seq pacbio -c 8 --region-parallel # Hia5 PacBio
fiberhmm-call -i aligned.bam -o calls.bam --enzyme hia5 --seq nanopore -c 8 --region-parallel # Hia5 Nanopore
fiberhmm-call -i aligned.bam -o calls.bam --enzyme dddb -c 8 --region-parallel # DddB DAF-seq (DddA: --enzyme ddda)
fiberhmm-extract -i calls.bam -o tracks/ # BED12 / bigBed tracks
A synthetic demo data set and a walk-through of every chemistry are in the Quick start.
Documentation
- Getting started:
installation, quick start, choosing
--enzymeand--seq - Concepts: how FiberHMM works, chemistries and platforms, coordinate frames, tags and scores
- Workflows:
calling, re-calling, DAF-seq, duplex pairing, tracks, QC, footprint classes
(
fiberhmm-consensus), transfer, strand rescue, training - Reference: every command and option, BAM tags, header declarations, bundled models, consensus output files, Python API
- Troubleshooting
License
MIT; see LICENSE. Citing FiberHMM.
1 maintainer
Metadata
1 maintainer
Release files for fiberhmm 3.0.0
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| File | Size | Uploaded | |
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| fiberhmm-3.0.0.tar.gz | 5.7 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| fiberhmm-3.0.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 8.9 MB
Release files / fiberhmm-3.0.0.tar.gz
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