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Hammerpede: training profile HMMs for primers from real Nanopore data

Hammerpede is a package to build strand-specific profile HMMs for a set of primers from real Oxford Nanopore Technologies' reads. The models built can be used by the pychopper package to identify and orient full length cDNA reads.

Getting Started

Dependencies

The required Python packages are installed by either pip or conda. The profile HMM alignment backend depends on the latest hmmer package. This can be easily installed using conda:

conda install -c bioconda hmmer

The package also requires the latest spoa. This is best to be installed from source according to the developers instructions.

Installation

Install via pip:

pip install git+https://github.com/nanoporetech/hammerpede.git

After installing the test can be run by issuing:

make test

Issue make help to get a list of make targets.

Usage

usage: hp_bootstrap.py [-h] -f query_fasta -o outdir [-i input_format]
                       [-g aln_params] [-s min_score]
                       input_fastx

Tool train strand-specific profile HMMs of primers from real Nanopore reads.

positional arguments:
  input_fastx      Input read fastq.

optional arguments:
  -h, --help       show this help message and exit
  -f query_fasta   Fasta with primer sequences.
  -o outdir        Output directory.
  -i input_format  Input/output format (fastq).
  -g aln_params    Alignment parameters (match, mismatch,gap_open,gap_extend).
  -s min_score     Score cutoff (0.8).

Example usage (see also test/Makefile):

hp_bootstrap.py -f cDNA_SSP_VNP_full.fas -o test_output -s 0.75 SIRV_E0_pcs109_1k.fq

The profile HMMs produced can be visualized using Skyling. For example, the VNP primer logo might look like this:

Contributing

• Please fork the repository and create a merge request to contribute.
• Use bumpversion to manage package versioning.
• The code should be PEP8 compliant, which can be tested by make lint.

Help

Licence and Copyright

(c) 2019 Oxford Nanopore Technologies Ltd.

This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/.

FAQs and tips

References and Supporting Information

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.

See the post announcing the tools at the Oxford Nanopore Technologies Community here.