We have a new bioinformatic resource that largely replaces the functionality of this project! See our new repository here: https://github.com/epi2me-labs/modbam2bed
This repository is now unsupported and we do not recommend its use. Please contact Oxford Nanopore: support@nanoporetech.com for help with your application if it is not possible to upgrade to our new resources, or we are missing key features.
Fast5mod is a set of two programs for converting Guppy's modified base Fast5 output into:
- An aligned or unaligned BAM formatted file, and
- Aggregate modified base calls.
The functionality was originally part of Medaka, but has be removed to this distinct project.
© 2020 Oxford Nanopore Technologies Ltd.
fast5mod is available on PyPI and can be installed using pip:
pip install fast5mod
We recommend using fast5mod within a virtual environment, viz.:
virtualenv fast5mod --python=python3 --prompt "(fast5mod) "
. fast5mod/bin/activate
pip install fast5mod
The basic workflow for aggregating Guppy basecalling results for Dcm, Dam, and CpG methylation is shown below.
Aggregating the information from Guppy outputs is a two stage process, first
the basecalling results are extracted .fast5 files and placed in a .bam
file:
FAST5PATH=guppy/workspace
REFERENCE=grch38.fasta
OUTBAM=meth.bam
fast5mod guppy2sam ${FAST5PATH} ${REFERENCE} \
--workers 74 --recursive \
| samtools sort -@ 8 | samtools view -b -@ 8 > ${OUTBAM}
samtools sort ${OUTBAM}
This program will extract both the basecall sequence and methylation scores, align the basecall to the reference, and store results in a standard format. In this preliminary workflow the methylation scores are stored in two SAM tags, 'MC' and 'MA', one each for 5mC and 6mA respectively. The tags are 8bit integer array-values, one value per basecall position. This is a different form to that proposed in the current hts-specs proposition, but allows for more trivial parsing.
The second step is to aggregate the reference-aligned information to produce a simple tabular summary of read methylation counts:
BAM=meth.bam
REFERENCE=grch38.fasta
REGION=chr20:500000-1000000
OUTPUT=meth.tsv
fast5mod call --meth cpg ${BAM} ${REFERENCE} ${REGION} ${OUTPUT}
Here the option --meth cpg indicates that loci containing the sequence
motif CG should be examined for 5mC presence. Other choices are
dcm for which the motifs CCAGG and CCTGG are examined for 5mC and dam
(GATC) for 6mA.
The output file is a simple tab-delimited text file with columns: 'ref.name', 'position', 'motif', 'fwd.meth.count', 'rev.meth.count', 'fwd.canon.count', and 'rev.canon.count'. Here fwd./ref. indicate counts on the two DNA strands and meth./canon. indicate counts for methylated and canonical bases. Note that the position field records the position of the first base in the motif recorded.
Licence and Copyright
© 2020 Oxford Nanopore Technologies Ltd.
fast5mod is distributed under the terms of the Mozilla Public License 2.0.
Research Release
Research releases are provided as technology demonstrators to provide early access to features or stimulate Community development of tools. Support for this software will be minimal and is only provided directly by the developers. Feature requests, improvements, and discussions are welcome and can be implemented by forking and pull requests. However much as we would like to rectify every issue and piece of feedback users may have, the developers may have limited resource for support of this software. Research releases may be unstable and subject to rapid iteration by Oxford Nanopore Technologies.